Starting phenix.real_space_refine on Wed Mar 4 21:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.map" model { file = "/net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m19_23616/03_2026/7m19_23616.cif" } resolution = 3.69 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= 0.002 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: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10639 2.51 5 N 2532 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16039 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'PEE': 3, 'YNJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.77, per 1000 atoms: 0.24 Number of scatterers: 16039 At special positions: 0 Unit cell: (110.289, 101.193, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.04 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 630.4 milliseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 11 sheets defined 74.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.668A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 23 through 49 removed outlier: 3.509A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 120 through 146 Proline residue: A 126 - end of helix removed outlier: 4.406A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.403A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.013A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.642A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.611A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.618A pdb=" N LEU A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.820A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 Processing helix chain 'B' and resid 26 through 49 removed outlier: 3.811A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.540A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 146 removed outlier: 3.739A pdb=" N PHE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.805A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.462A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 4.097A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 258 through 286 removed outlier: 3.959A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 347 removed outlier: 4.021A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.906A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.495A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.687A pdb=" N PHE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.620A pdb=" N PHE C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.888A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 4.770A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.382A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.999A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.514A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.998A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 4.012A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.898A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.168A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 22 removed outlier: 4.113A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Proline residue: D 22 - end of helix Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.631A pdb=" N PHE D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.739A pdb=" N ARG D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 146 removed outlier: 3.544A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.093A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.324A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.008A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 255 removed outlier: 3.501A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.802A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.966A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.649A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.583A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Proline residue: E 22 - end of helix Processing helix chain 'E' and resid 23 through 49 removed outlier: 3.534A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.510A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 146 removed outlier: 3.644A pdb=" N PHE E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.561A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.449A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.747A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 3.726A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.167A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.601A pdb=" N PHE F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 removed outlier: 3.581A pdb=" N ARG F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 146 removed outlier: 3.638A pdb=" N PHE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.628A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.071A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 4.120A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 Processing helix chain 'F' and resid 258 through 286 removed outlier: 3.844A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.535A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.367A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.891A pdb=" N VAL D 293 " --> pdb=" O CYS D 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.555A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.814A pdb=" N VAL F 293 " --> pdb=" O CYS F 310 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2949 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: 2.58 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2379 1.31 - 1.44: 4937 1.44 - 1.57: 9006 1.57 - 1.69: 5 1.69 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C18 PEE C 903 " pdb=" C19 PEE C 903 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE F 902 " pdb=" C19 PEE F 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE C 904 " pdb=" C19 PEE C 904 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE E 902 " pdb=" C19 PEE E 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 21581 2.46 - 4.91: 491 4.91 - 7.37: 75 7.37 - 9.82: 37 9.82 - 12.28: 38 Bond angle restraints: 22222 Sorted by residual: angle pdb=" C THR E 48 " pdb=" N GLN E 49 " pdb=" CA GLN E 49 " ideal model delta sigma weight residual 121.90 114.34 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" N GLU E 154 " pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " ideal model delta sigma weight residual 110.28 118.21 -7.93 1.55e+00 4.16e-01 2.62e+01 angle pdb=" C ASN F 370 " pdb=" N ASP F 371 " pdb=" CA ASP F 371 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLU F 245 " pdb=" N LYS F 246 " pdb=" CA LYS F 246 " ideal model delta sigma weight residual 120.68 113.66 7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C CYS B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta sigma weight residual 122.36 115.31 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 9067 24.81 - 49.61: 640 49.61 - 74.42: 45 74.42 - 99.23: 14 99.23 - 124.03: 8 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER D 352 " pdb=" C SER D 352 " pdb=" N PHE D 353 " pdb=" CA PHE D 353 " ideal model delta harmonic sigma weight residual 180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C12 PEE B 902 " pdb=" C10 PEE B 902 " pdb=" C11 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sinusoidal sigma weight residual -19.47 104.56 -124.03 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1922 0.062 - 0.124: 434 0.124 - 0.186: 48 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CB VAL E 297 " pdb=" CA VAL E 297 " pdb=" CG1 VAL E 297 " pdb=" CG2 VAL E 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C05 YNJ C 902 " pdb=" C06 YNJ C 902 " pdb=" C13 YNJ C 902 " pdb=" C27 YNJ C 902 " both_signs ideal model delta sigma weight residual False 3.00 2.70 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 275 " -0.018 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 275 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 275 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 275 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 275 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 244 " -0.018 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE E 244 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 244 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 244 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 244 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 244 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 136 " -0.020 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE C 136 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 136 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 136 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 136 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2744 2.77 - 3.30: 15064 3.30 - 3.83: 26554 3.83 - 4.37: 28621 4.37 - 4.90: 50238 Nonbonded interactions: 123221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.231 3.040 nonbonded pdb=" O THR D 44 " pdb=" OG1 THR D 48 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP E 50 " pdb=" OH TYR E 114 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP C 50 " pdb=" OH TYR C 114 " model vdw 2.273 3.040 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.273 3.040 ... (remaining 123216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 408 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or resid 903)) selection = (chain 'B' and (resid 15 through 901 or (resid 903 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 901 or (resid 903 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )))) selection = (chain 'D' and (resid 15 through 901 or (resid 903 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )))) selection = (chain 'E' and (resid 15 through 901 or (resid 903 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )))) selection = (chain 'F' and (resid 15 through 901 or (resid 903 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.500 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.183 16491 Z= 0.470 Angle : 1.030 12.279 22258 Z= 0.508 Chirality : 0.052 0.310 2408 Planarity : 0.005 0.042 2673 Dihedral : 15.738 124.033 6060 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.19), residues: 1842 helix: 0.04 (0.14), residues: 1236 sheet: 0.66 (0.49), residues: 96 loop : -1.95 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 357 TYR 0.022 0.002 TYR A 332 PHE 0.057 0.002 PHE D 275 TRP 0.026 0.002 TRP D 143 HIS 0.019 0.002 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00946 (16473) covalent geometry : angle 1.03056 (22222) SS BOND : bond 0.00286 ( 18) SS BOND : angle 0.71087 ( 36) hydrogen bonds : bond 0.11051 ( 1005) hydrogen bonds : angle 5.31539 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8215 (tmt-80) cc_final: 0.7964 (tpt170) REVERT: B 325 TYR cc_start: 0.8747 (t80) cc_final: 0.8428 (t80) REVERT: C 336 CYS cc_start: 0.8318 (m) cc_final: 0.8114 (t) REVERT: D 37 MET cc_start: 0.8513 (ptp) cc_final: 0.8311 (ptt) REVERT: D 351 TYR cc_start: 0.6384 (t80) cc_final: 0.5922 (t80) REVERT: D 399 GLU cc_start: 0.8353 (mp0) cc_final: 0.7554 (mp0) REVERT: E 162 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8758 (mmtm) REVERT: F 249 LYS cc_start: 0.9154 (tptt) cc_final: 0.8574 (pttt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1252 time to fit residues: 49.4774 Evaluate side-chains 187 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 155 HIS A 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103108 restraints weight = 36021.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104157 restraints weight = 14414.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105002 restraints weight = 9385.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105170 restraints weight = 8084.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105306 restraints weight = 7667.822| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16491 Z= 0.128 Angle : 0.552 11.132 22258 Z= 0.299 Chirality : 0.040 0.136 2408 Planarity : 0.003 0.032 2673 Dihedral : 9.448 84.083 2298 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 8.99 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.20), residues: 1842 helix: 1.04 (0.15), residues: 1254 sheet: 1.05 (0.50), residues: 96 loop : -1.52 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.014 0.001 TYR D 332 PHE 0.019 0.001 PHE C 136 TRP 0.021 0.001 TRP F 143 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00273 (16473) covalent geometry : angle 0.55200 (22222) SS BOND : bond 0.00254 ( 18) SS BOND : angle 0.66649 ( 36) hydrogen bonds : bond 0.04441 ( 1005) hydrogen bonds : angle 3.95035 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8010 (tmt-80) cc_final: 0.7767 (tpt170) REVERT: A 288 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.9130 (t0) REVERT: B 325 TYR cc_start: 0.8816 (t80) cc_final: 0.8465 (t80) REVERT: C 161 LEU cc_start: 0.8796 (mm) cc_final: 0.8522 (mm) REVERT: D 238 GLU cc_start: 0.8580 (tp30) cc_final: 0.7711 (pp20) REVERT: D 399 GLU cc_start: 0.8405 (mp0) cc_final: 0.7894 (mp0) REVERT: E 18 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7575 (ptp90) REVERT: E 162 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8576 (mmtm) REVERT: E 255 GLU cc_start: 0.8416 (tp30) cc_final: 0.8149 (tp30) REVERT: F 29 ASP cc_start: 0.8535 (t0) cc_final: 0.8319 (t0) REVERT: F 154 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8454 (mm-30) REVERT: F 249 LYS cc_start: 0.9168 (tptt) cc_final: 0.8600 (pttt) REVERT: F 289 ILE cc_start: 0.8941 (pt) cc_final: 0.8728 (mt) outliers start: 30 outliers final: 13 residues processed: 238 average time/residue: 0.1238 time to fit residues: 45.4206 Evaluate side-chains 199 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS B 288 ASN E 116 ASN E 155 HIS E 287 HIS E 288 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099256 restraints weight = 36707.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101844 restraints weight = 15375.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103195 restraints weight = 8413.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103325 restraints weight = 6921.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103499 restraints weight = 6152.219| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16491 Z= 0.168 Angle : 0.571 10.005 22258 Z= 0.308 Chirality : 0.041 0.199 2408 Planarity : 0.003 0.036 2673 Dihedral : 8.075 67.847 2298 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.23 % Allowed : 14.03 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.21), residues: 1842 helix: 1.32 (0.15), residues: 1284 sheet: 1.39 (0.50), residues: 96 loop : -1.70 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.017 0.001 TYR E 351 PHE 0.019 0.001 PHE C 136 TRP 0.018 0.001 TRP C 143 HIS 0.009 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00381 (16473) covalent geometry : angle 0.57087 (22222) SS BOND : bond 0.00302 ( 18) SS BOND : angle 0.68357 ( 36) hydrogen bonds : bond 0.04566 ( 1005) hydrogen bonds : angle 3.86065 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8183 (tmt-80) cc_final: 0.7881 (tpt170) REVERT: B 288 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8692 (t0) REVERT: B 325 TYR cc_start: 0.8866 (t80) cc_final: 0.8605 (t80) REVERT: C 161 LEU cc_start: 0.8849 (mm) cc_final: 0.8553 (mm) REVERT: D 161 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7608 (pp) REVERT: D 280 CYS cc_start: 0.8791 (m) cc_final: 0.8442 (m) REVERT: E 18 ARG cc_start: 0.8033 (ptp-170) cc_final: 0.7484 (ptp90) REVERT: E 162 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8561 (mmtm) REVERT: F 154 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8359 (mm-30) REVERT: F 245 GLU cc_start: 0.8836 (mp0) cc_final: 0.8421 (mp0) REVERT: F 249 LYS cc_start: 0.9210 (tptt) cc_final: 0.8649 (pttt) REVERT: F 289 ILE cc_start: 0.8997 (pt) cc_final: 0.8788 (mt) REVERT: F 381 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8034 (mm-40) outliers start: 39 outliers final: 26 residues processed: 210 average time/residue: 0.1229 time to fit residues: 39.9482 Evaluate side-chains 204 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100296 restraints weight = 36473.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102894 restraints weight = 15611.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104866 restraints weight = 8543.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104839 restraints weight = 6836.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104919 restraints weight = 5914.217| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16491 Z= 0.145 Angle : 0.542 9.113 22258 Z= 0.293 Chirality : 0.041 0.178 2408 Planarity : 0.003 0.028 2673 Dihedral : 7.548 65.439 2298 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.81 % Allowed : 15.52 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1842 helix: 1.60 (0.15), residues: 1260 sheet: 1.52 (0.51), residues: 96 loop : -1.33 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.014 0.001 TYR E 351 PHE 0.022 0.001 PHE F 244 TRP 0.016 0.001 TRP C 143 HIS 0.010 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00325 (16473) covalent geometry : angle 0.54205 (22222) SS BOND : bond 0.00265 ( 18) SS BOND : angle 0.65056 ( 36) hydrogen bonds : bond 0.04298 ( 1005) hydrogen bonds : angle 3.76671 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8185 (tmt-80) cc_final: 0.7883 (tpt170) REVERT: A 399 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: B 269 ILE cc_start: 0.8755 (tt) cc_final: 0.8549 (tp) REVERT: B 325 TYR cc_start: 0.8846 (t80) cc_final: 0.8607 (t80) REVERT: C 161 LEU cc_start: 0.8822 (mm) cc_final: 0.8537 (mm) REVERT: D 161 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7608 (pp) REVERT: D 399 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: E 162 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8600 (mmtm) REVERT: E 399 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7726 (mm-30) REVERT: F 154 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8348 (mm-30) REVERT: F 245 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: F 249 LYS cc_start: 0.9197 (tptt) cc_final: 0.8632 (pttt) REVERT: F 380 ASP cc_start: 0.8110 (t70) cc_final: 0.7568 (t0) REVERT: F 381 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8179 (mm-40) outliers start: 49 outliers final: 35 residues processed: 219 average time/residue: 0.1228 time to fit residues: 41.5909 Evaluate side-chains 220 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 245 GLU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS E 155 HIS F 288 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101343 restraints weight = 35980.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104043 restraints weight = 15011.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105731 restraints weight = 8071.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105724 restraints weight = 6614.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105957 restraints weight = 5707.648| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16491 Z= 0.125 Angle : 0.530 9.721 22258 Z= 0.285 Chirality : 0.040 0.155 2408 Planarity : 0.003 0.028 2673 Dihedral : 7.185 63.821 2298 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.38 % Allowed : 15.81 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1842 helix: 1.70 (0.15), residues: 1260 sheet: 1.64 (0.51), residues: 96 loop : -1.30 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.012 0.001 TYR B 332 PHE 0.036 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.012 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00274 (16473) covalent geometry : angle 0.53017 (22222) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.58245 ( 36) hydrogen bonds : bond 0.04107 ( 1005) hydrogen bonds : angle 3.68656 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8132 (tmt-80) cc_final: 0.7827 (tpt170) REVERT: B 269 ILE cc_start: 0.8746 (tt) cc_final: 0.8541 (tp) REVERT: B 325 TYR cc_start: 0.8842 (t80) cc_final: 0.8581 (t80) REVERT: C 161 LEU cc_start: 0.8826 (mm) cc_final: 0.8499 (mm) REVERT: D 161 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7577 (pp) REVERT: D 280 CYS cc_start: 0.8807 (m) cc_final: 0.8558 (m) REVERT: D 399 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: E 18 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7504 (ptp90) REVERT: E 133 THR cc_start: 0.9522 (m) cc_final: 0.9217 (t) REVERT: E 162 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8593 (mmtm) REVERT: E 255 GLU cc_start: 0.8279 (tp30) cc_final: 0.8068 (tp30) REVERT: E 399 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7872 (mm-30) REVERT: F 154 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8339 (mm-30) REVERT: F 245 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: F 249 LYS cc_start: 0.9192 (tptt) cc_final: 0.8624 (pttt) REVERT: F 380 ASP cc_start: 0.8085 (t70) cc_final: 0.7508 (t0) outliers start: 59 outliers final: 42 residues processed: 236 average time/residue: 0.1219 time to fit residues: 44.5042 Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 245 GLU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 28 optimal weight: 0.0870 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS D 155 HIS E 105 GLN E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103318 restraints weight = 36573.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104340 restraints weight = 14856.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104837 restraints weight = 10732.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105096 restraints weight = 9199.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105296 restraints weight = 8463.673| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16491 Z= 0.118 Angle : 0.530 9.103 22258 Z= 0.285 Chirality : 0.040 0.170 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.823 61.989 2298 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.81 % Allowed : 17.75 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1842 helix: 1.76 (0.15), residues: 1260 sheet: 1.70 (0.51), residues: 96 loop : -1.32 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.014 0.001 TYR E 332 PHE 0.027 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.010 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00255 (16473) covalent geometry : angle 0.53004 (22222) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.53782 ( 36) hydrogen bonds : bond 0.03939 ( 1005) hydrogen bonds : angle 3.63805 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8168 (tmt-80) cc_final: 0.7848 (tpt170) REVERT: B 269 ILE cc_start: 0.8746 (tt) cc_final: 0.8536 (tp) REVERT: B 325 TYR cc_start: 0.8823 (t80) cc_final: 0.8536 (t80) REVERT: C 161 LEU cc_start: 0.8826 (mm) cc_final: 0.8542 (mm) REVERT: C 330 ILE cc_start: 0.9482 (mm) cc_final: 0.9265 (tt) REVERT: D 161 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7537 (pp) REVERT: D 280 CYS cc_start: 0.8784 (m) cc_final: 0.8568 (m) REVERT: E 18 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7510 (ptp90) REVERT: E 133 THR cc_start: 0.9513 (m) cc_final: 0.9234 (t) REVERT: E 162 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8578 (mmtm) REVERT: E 168 TRP cc_start: 0.7315 (t60) cc_final: 0.6759 (t60) REVERT: E 255 GLU cc_start: 0.8210 (tp30) cc_final: 0.7885 (tp30) REVERT: E 399 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7936 (mm-30) REVERT: F 249 LYS cc_start: 0.9194 (tptt) cc_final: 0.8620 (pttt) REVERT: F 328 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (tt) REVERT: F 380 ASP cc_start: 0.8066 (t70) cc_final: 0.7529 (t0) outliers start: 49 outliers final: 39 residues processed: 239 average time/residue: 0.1209 time to fit residues: 44.8940 Evaluate side-chains 223 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102855 restraints weight = 36201.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103777 restraints weight = 14317.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104321 restraints weight = 10140.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104679 restraints weight = 8635.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104779 restraints weight = 7995.296| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16491 Z= 0.130 Angle : 0.544 8.849 22258 Z= 0.292 Chirality : 0.041 0.217 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.613 60.884 2298 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.49 % Allowed : 17.93 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1842 helix: 1.79 (0.15), residues: 1260 sheet: 1.84 (0.51), residues: 96 loop : -1.31 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.013 0.001 TYR E 332 PHE 0.044 0.001 PHE F 244 TRP 0.019 0.001 TRP C 342 HIS 0.012 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00288 (16473) covalent geometry : angle 0.54436 (22222) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.57661 ( 36) hydrogen bonds : bond 0.03981 ( 1005) hydrogen bonds : angle 3.65641 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8119 (tmt-80) cc_final: 0.7814 (tpt170) REVERT: B 288 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8670 (t0) REVERT: B 325 TYR cc_start: 0.8831 (t80) cc_final: 0.8558 (t80) REVERT: C 161 LEU cc_start: 0.8820 (mm) cc_final: 0.8530 (mm) REVERT: D 161 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7657 (pp) REVERT: D 280 CYS cc_start: 0.8754 (m) cc_final: 0.8505 (m) REVERT: D 353 PHE cc_start: 0.6321 (OUTLIER) cc_final: 0.5694 (t80) REVERT: E 133 THR cc_start: 0.9518 (m) cc_final: 0.9238 (t) REVERT: E 162 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8592 (mmtm) REVERT: E 168 TRP cc_start: 0.7367 (t60) cc_final: 0.6858 (t60) REVERT: E 255 GLU cc_start: 0.8305 (tp30) cc_final: 0.7958 (tp30) REVERT: E 399 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7875 (mm-30) REVERT: F 249 LYS cc_start: 0.9179 (tptt) cc_final: 0.8602 (pttt) REVERT: F 328 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7969 (tt) REVERT: F 337 MET cc_start: 0.8684 (mmm) cc_final: 0.7986 (tmm) REVERT: F 380 ASP cc_start: 0.8084 (t70) cc_final: 0.7585 (t0) REVERT: F 381 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8139 (mm-40) outliers start: 61 outliers final: 45 residues processed: 232 average time/residue: 0.1230 time to fit residues: 44.0515 Evaluate side-chains 226 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 HIS E 155 HIS E 288 ASN F 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100493 restraints weight = 36539.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103191 restraints weight = 15581.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105017 restraints weight = 8398.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105095 restraints weight = 6703.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105104 restraints weight = 5770.792| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16491 Z= 0.144 Angle : 0.566 9.782 22258 Z= 0.301 Chirality : 0.041 0.177 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.491 60.090 2298 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.26 % Allowed : 18.84 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1842 helix: 1.78 (0.15), residues: 1260 sheet: 1.95 (0.51), residues: 96 loop : -1.27 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.012 0.001 TYR B 332 PHE 0.035 0.001 PHE F 244 TRP 0.016 0.001 TRP C 342 HIS 0.012 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00326 (16473) covalent geometry : angle 0.56552 (22222) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.60336 ( 36) hydrogen bonds : bond 0.04099 ( 1005) hydrogen bonds : angle 3.68561 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8228 (tmt-80) cc_final: 0.7906 (tpt170) REVERT: B 325 TYR cc_start: 0.8839 (t80) cc_final: 0.8569 (t80) REVERT: C 161 LEU cc_start: 0.8823 (mm) cc_final: 0.8539 (mm) REVERT: C 330 ILE cc_start: 0.9472 (mm) cc_final: 0.9243 (tt) REVERT: D 161 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7643 (pp) REVERT: D 280 CYS cc_start: 0.8739 (m) cc_final: 0.8480 (m) REVERT: D 353 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5428 (t80) REVERT: E 18 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7523 (ptp90) REVERT: E 133 THR cc_start: 0.9516 (m) cc_final: 0.9246 (t) REVERT: E 162 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8617 (mmtm) REVERT: E 168 TRP cc_start: 0.7350 (t60) cc_final: 0.6782 (t60) REVERT: E 255 GLU cc_start: 0.8244 (tp30) cc_final: 0.7892 (tp30) REVERT: E 288 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8794 (m-40) REVERT: E 399 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7936 (mm-30) REVERT: F 249 LYS cc_start: 0.9184 (tptt) cc_final: 0.8656 (pptt) REVERT: F 328 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7907 (tt) REVERT: F 337 MET cc_start: 0.8673 (mmm) cc_final: 0.7984 (tmm) REVERT: F 381 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8066 (mm-40) outliers start: 57 outliers final: 47 residues processed: 215 average time/residue: 0.1209 time to fit residues: 40.4155 Evaluate side-chains 224 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS D 400 ASN E 155 HIS E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102212 restraints weight = 35987.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105474 restraints weight = 16902.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.107642 restraints weight = 8674.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.107604 restraints weight = 6091.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.107651 restraints weight = 5776.248| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16491 Z= 0.112 Angle : 0.545 9.049 22258 Z= 0.289 Chirality : 0.040 0.250 2408 Planarity : 0.003 0.029 2673 Dihedral : 6.217 59.478 2298 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.63 % Allowed : 19.70 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.21), residues: 1842 helix: 1.83 (0.15), residues: 1260 sheet: 1.99 (0.51), residues: 96 loop : -1.30 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.010 0.001 TYR B 332 PHE 0.032 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.011 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00239 (16473) covalent geometry : angle 0.54469 (22222) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.50570 ( 36) hydrogen bonds : bond 0.03784 ( 1005) hydrogen bonds : angle 3.60683 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8188 (tmt-80) cc_final: 0.7853 (tpt170) REVERT: B 143 TRP cc_start: 0.8509 (t60) cc_final: 0.8152 (t60) REVERT: B 325 TYR cc_start: 0.8787 (t80) cc_final: 0.8485 (t80) REVERT: C 161 LEU cc_start: 0.8824 (mm) cc_final: 0.8554 (mm) REVERT: C 330 ILE cc_start: 0.9471 (mm) cc_final: 0.9268 (tt) REVERT: D 280 CYS cc_start: 0.8718 (m) cc_final: 0.8466 (m) REVERT: D 353 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5543 (t80) REVERT: E 18 ARG cc_start: 0.7943 (ptp-170) cc_final: 0.7562 (ptp90) REVERT: E 133 THR cc_start: 0.9482 (m) cc_final: 0.9237 (t) REVERT: E 162 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8591 (mmtm) REVERT: E 168 TRP cc_start: 0.7339 (t60) cc_final: 0.6821 (t60) REVERT: E 255 GLU cc_start: 0.8334 (tp30) cc_final: 0.7963 (tp30) REVERT: E 288 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8768 (m-40) REVERT: E 399 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7921 (mm-30) REVERT: F 249 LYS cc_start: 0.9215 (tptt) cc_final: 0.8617 (pttt) REVERT: F 328 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7969 (tt) REVERT: F 337 MET cc_start: 0.8632 (mmm) cc_final: 0.8050 (tmm) outliers start: 46 outliers final: 40 residues processed: 234 average time/residue: 0.1169 time to fit residues: 42.4624 Evaluate side-chains 230 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 132 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 288 ASN E 105 GLN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098866 restraints weight = 36209.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102277 restraints weight = 16358.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104032 restraints weight = 8451.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104130 restraints weight = 7068.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104163 restraints weight = 6021.039| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16491 Z= 0.168 Angle : 0.601 9.310 22258 Z= 0.318 Chirality : 0.042 0.236 2408 Planarity : 0.003 0.026 2673 Dihedral : 6.404 58.695 2298 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.81 % Allowed : 19.87 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1842 helix: 1.79 (0.15), residues: 1260 sheet: 2.02 (0.51), residues: 96 loop : -1.22 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.031 0.001 TYR D 325 PHE 0.032 0.001 PHE F 244 TRP 0.014 0.001 TRP D 143 HIS 0.012 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00384 (16473) covalent geometry : angle 0.60059 (22222) SS BOND : bond 0.00293 ( 18) SS BOND : angle 0.68991 ( 36) hydrogen bonds : bond 0.04246 ( 1005) hydrogen bonds : angle 3.76832 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8261 (tmt-80) cc_final: 0.7932 (tpt170) REVERT: B 288 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8676 (t0) REVERT: B 325 TYR cc_start: 0.8858 (t80) cc_final: 0.8586 (t80) REVERT: C 161 LEU cc_start: 0.8839 (mm) cc_final: 0.8570 (mm) REVERT: C 245 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8854 (mm-30) REVERT: C 330 ILE cc_start: 0.9524 (mm) cc_final: 0.9277 (tt) REVERT: D 280 CYS cc_start: 0.8731 (m) cc_final: 0.8483 (m) REVERT: D 353 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5250 (t80) REVERT: E 18 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7454 (ptp90) REVERT: E 133 THR cc_start: 0.9526 (m) cc_final: 0.9233 (t) REVERT: E 168 TRP cc_start: 0.7440 (t60) cc_final: 0.6875 (t60) REVERT: E 288 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (m-40) REVERT: F 249 LYS cc_start: 0.9234 (tptt) cc_final: 0.8584 (pttt) REVERT: F 328 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7962 (tt) outliers start: 49 outliers final: 42 residues processed: 210 average time/residue: 0.1147 time to fit residues: 37.8829 Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 95 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS E 105 GLN E 155 HIS E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.129097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101561 restraints weight = 35701.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104648 restraints weight = 16554.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106725 restraints weight = 8511.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106638 restraints weight = 6836.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106722 restraints weight = 5937.884| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16491 Z= 0.125 Angle : 0.573 9.715 22258 Z= 0.303 Chirality : 0.041 0.231 2408 Planarity : 0.003 0.028 2673 Dihedral : 6.235 57.965 2298 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.75 % Allowed : 20.10 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1842 helix: 1.81 (0.15), residues: 1260 sheet: 2.04 (0.51), residues: 96 loop : -1.21 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.030 0.001 TYR D 325 PHE 0.030 0.001 PHE F 244 TRP 0.016 0.001 TRP C 143 HIS 0.017 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00277 (16473) covalent geometry : angle 0.57263 (22222) SS BOND : bond 0.00217 ( 18) SS BOND : angle 0.58644 ( 36) hydrogen bonds : bond 0.03998 ( 1005) hydrogen bonds : angle 3.69705 ( 2949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.20 seconds wall clock time: 43 minutes 14.10 seconds (2594.10 seconds total)