Starting phenix.real_space_refine on Fri Jul 3 21:54:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m19_23616/07_2026/7m19_23616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m19_23616/07_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_23616/07_2026/7m19_23616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m19_23616/07_2026/7m19_23616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m19_23616/07_2026/7m19_23616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m19_23616/07_2026/7m19_23616.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m19_23616/07_2026/7m19_23616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m19_23616/07_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-6108/lib/python3.11/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: 78 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: 78 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: 78 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: 78 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: 78 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: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.63, per 1000 atoms: 0.23 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: 1.05 Conformation dependent library (CDL) restraints added in 832.8 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: 0.40 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: 2.88 Time building geometry restraints manager: 1.43 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: 9047 24.81 - 49.61: 638 49.61 - 74.42: 45 74.42 - 99.23: 14 99.23 - 124.03: 8 Dihedral angle restraints: 9752 sinusoidal: 4100 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 9749 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: 4.900 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 15.736 124.033 6038 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/Z covalent geometry : bond 0.00946 / 0.47 (16473) covalent geometry : angle 1.03056 / 0.51 (22222) SS BOND : bond 0.00286 / 0.18 ( 18) SS BOND : angle 0.71087 / 0.45 ( 36) hydrogen bonds : bond 0.11051 / 6.97 ( 1005) hydrogen bonds : angle 5.31539 / 3.76 ( 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 : 0.397 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: 0.1092 time to fit residues: 43.2617 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 : 0.502 ------------------------------------------------------------------------------- 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... A 105 GLN A 155 HIS A 288 ASN C 155 HIS E 155 HIS F 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.128474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103882 restraints weight = 35926.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103674 restraints weight = 14395.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104545 restraints weight = 11225.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104950 restraints weight = 8577.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105223 restraints weight = 7847.037| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1242 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 : 0.555 11.609 22258 Z= 0.300 Chirality : 0.040 0.139 2408 Planarity : 0.003 0.032 2673 Dihedral : 9.335 83.052 2276 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.49 % Allowed : 9.22 % 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: 0.54 (0.20), residues: 1842 helix: 1.04 (0.15), residues: 1254 sheet: 1.05 (0.50), residues: 96 loop : -1.51 (0.29), 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 0.022 0.001 TRP F 143 HIS 0.008 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (16473) covalent geometry : angle 0.55463 / 0.30 (22222) SS BOND : bond 0.00245 / 0.16 ( 18) SS BOND : angle 0.65315 / 0.43 ( 36) hydrogen bonds : bond 0.04420 / 2.89 ( 1005) hydrogen bonds : angle 3.95815 / 2.80 ( 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 247 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8093 (tmt-80) cc_final: 0.7815 (tpt170) REVERT: A 288 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.9133 (t0) REVERT: B 325 TYR cc_start: 0.8819 (t80) cc_final: 0.8483 (t80) REVERT: C 161 LEU cc_start: 0.8809 (mm) cc_final: 0.8531 (mm) REVERT: D 238 GLU cc_start: 0.8600 (tp30) cc_final: 0.7738 (pp20) REVERT: D 399 GLU cc_start: 0.8452 (mp0) cc_final: 0.7960 (mp0) REVERT: E 18 ARG cc_start: 0.8006 (ptp-170) cc_final: 0.7554 (ptp90) REVERT: E 162 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8585 (mmtm) REVERT: E 255 GLU cc_start: 0.8335 (tp30) cc_final: 0.8057 (tp30) REVERT: F 29 ASP cc_start: 0.8544 (t0) cc_final: 0.8330 (t0) REVERT: F 154 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8451 (mm-30) REVERT: F 249 LYS cc_start: 0.9183 (tptt) cc_final: 0.8597 (pttt) REVERT: F 289 ILE cc_start: 0.8938 (pt) cc_final: 0.8729 (mt) outliers start: 26 outliers final: 12 residues processed: 236 average time/residue: 0.1188 time to fit residues: 43.2586 Evaluate side-chains 196 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU 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: 0.3980 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 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: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS B 155 HIS B 253 HIS B 288 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.125794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098496 restraints weight = 36783.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100891 restraints weight = 15568.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102369 restraints weight = 8554.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102576 restraints weight = 6883.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102978 restraints weight = 6087.697| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1608 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= 0.177 Angle : 0.578 9.631 22258 Z= 0.312 Chirality : 0.042 0.204 2408 Planarity : 0.003 0.036 2673 Dihedral : 8.040 68.660 2276 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.18 % Allowed : 13.80 % Favored : 84.02 % 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: 0.84 (0.21), residues: 1842 helix: 1.30 (0.15), residues: 1284 sheet: 1.34 (0.50), residues: 96 loop : -1.72 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 309 TYR 0.016 0.001 TYR E 351 PHE 0.019 0.002 PHE C 136 TRP 0.018 0.001 TRP C 143 HIS 0.009 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (16473) covalent geometry : angle 0.57790 / 0.31 (22222) SS BOND : bond 0.00317 / 0.20 ( 18) SS BOND : angle 0.69212 / 0.47 ( 36) hydrogen bonds : bond 0.04608 / 3.01 ( 1005) hydrogen bonds : angle 3.88058 / 2.75 ( 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 226 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8182 (tmt-80) cc_final: 0.7882 (tpt170) REVERT: B 288 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8682 (t0) REVERT: B 325 TYR cc_start: 0.8873 (t80) cc_final: 0.8615 (t80) REVERT: C 161 LEU cc_start: 0.8855 (mm) cc_final: 0.8557 (mm) REVERT: D 161 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 280 CYS cc_start: 0.8793 (m) cc_final: 0.8437 (m) REVERT: E 162 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8555 (mmtm) REVERT: F 154 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8348 (mm-30) REVERT: F 245 GLU cc_start: 0.8833 (mp0) cc_final: 0.8413 (mp0) REVERT: F 249 LYS cc_start: 0.9207 (tptt) cc_final: 0.8646 (pttt) REVERT: F 381 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8033 (mm-40) outliers start: 38 outliers final: 23 residues processed: 209 average time/residue: 0.1094 time to fit residues: 35.4046 Evaluate side-chains 200 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 380 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 277 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 0.0060 chunk 164 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS B 155 HIS B 253 HIS E 155 HIS F 288 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101238 restraints weight = 36437.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103753 restraints weight = 15432.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105971 restraints weight = 8498.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105842 restraints weight = 6701.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105906 restraints weight = 5864.450| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16491 Z= 0.126 Angle : 0.527 9.149 22258 Z= 0.285 Chirality : 0.040 0.175 2408 Planarity : 0.003 0.031 2673 Dihedral : 7.368 67.599 2276 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.58 % Allowed : 15.52 % Favored : 81.90 % 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: 1.29 (0.21), residues: 1842 helix: 1.62 (0.15), residues: 1260 sheet: 1.51 (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 309 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/Z covalent geometry : bond 0.00276 / 0.13 (16473) covalent geometry : angle 0.52717 / 0.28 (22222) SS BOND : bond 0.00234 / 0.15 ( 18) SS BOND : angle 0.60659 / 0.40 ( 36) hydrogen bonds : bond 0.04123 / 2.70 ( 1005) hydrogen bonds : angle 3.71108 / 2.63 ( 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: 45 poor density : 195 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8159 (tmt-80) cc_final: 0.7858 (tpt170) REVERT: B 269 ILE cc_start: 0.8739 (tt) cc_final: 0.8529 (tp) REVERT: B 325 TYR cc_start: 0.8821 (t80) cc_final: 0.8598 (t80) REVERT: C 161 LEU cc_start: 0.8825 (mm) cc_final: 0.8536 (mm) REVERT: D 161 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7553 (pp) REVERT: E 18 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7740 (ptp90) REVERT: E 162 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8600 (mmtm) REVERT: E 255 GLU cc_start: 0.8292 (tp30) cc_final: 0.7936 (tp30) REVERT: E 399 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7701 (mm-30) REVERT: F 154 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8346 (mm-30) REVERT: F 245 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: F 249 LYS cc_start: 0.9194 (tptt) cc_final: 0.8624 (pttt) REVERT: F 380 ASP cc_start: 0.8075 (t70) cc_final: 0.7500 (t0) outliers start: 45 outliers final: 29 residues processed: 220 average time/residue: 0.1192 time to fit residues: 40.4433 Evaluate side-chains 208 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 C residue 104 HIS Chi-restraints excluded: chain C residue 130 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 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 E residue 40 VAL 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 155 HIS Chi-restraints excluded: chain F residue 245 GLU Chi-restraints excluded: chain F residue 330 ILE 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: 0.7980 chunk 129 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 156 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN E 105 GLN E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101847 restraints weight = 35881.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104614 restraints weight = 14887.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106273 restraints weight = 7949.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106359 restraints weight = 6364.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106435 restraints weight = 5543.288| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1901 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= 0.121 Angle : 0.530 9.835 22258 Z= 0.285 Chirality : 0.040 0.158 2408 Planarity : 0.003 0.031 2673 Dihedral : 7.039 66.444 2276 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.21 % Allowed : 16.32 % Favored : 80.47 % 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: 1.44 (0.21), residues: 1842 helix: 1.74 (0.15), residues: 1260 sheet: 1.69 (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 309 TYR 0.011 0.001 TYR B 332 PHE 0.038 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.014 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16473) covalent geometry : angle 0.53005 / 0.28 (22222) SS BOND : bond 0.00217 / 0.14 ( 18) SS BOND : angle 0.57828 / 0.39 ( 36) hydrogen bonds : bond 0.04035 / 2.65 ( 1005) hydrogen bonds : angle 3.66635 / 2.60 ( 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 260 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8119 (tmt-80) cc_final: 0.7812 (tpt170) REVERT: B 269 ILE cc_start: 0.8741 (tt) cc_final: 0.8532 (tp) REVERT: B 325 TYR cc_start: 0.8826 (t80) cc_final: 0.8543 (t80) REVERT: C 161 LEU cc_start: 0.8817 (mm) cc_final: 0.8495 (mm) REVERT: D 161 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7572 (pp) REVERT: D 280 CYS cc_start: 0.8813 (m) cc_final: 0.8559 (m) REVERT: E 18 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7613 (ptp90) REVERT: E 162 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8595 (mmtm) REVERT: E 255 GLU cc_start: 0.8301 (tp30) cc_final: 0.8087 (tp30) REVERT: E 399 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 154 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8344 (mm-30) REVERT: F 245 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: F 249 LYS cc_start: 0.9190 (tptt) cc_final: 0.8670 (pptt) REVERT: F 380 ASP cc_start: 0.8069 (t70) cc_final: 0.7540 (t0) REVERT: F 381 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8113 (mm-40) outliers start: 56 outliers final: 40 residues processed: 238 average time/residue: 0.1158 time to fit residues: 42.7221 Evaluate side-chains 217 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 408 ASN 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 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 245 GLU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 330 ILE 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: 0.0270 chunk 75 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS D 155 HIS E 116 ASN 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 = 0.3846 r_free = 0.3846 target = 0.129309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103881 restraints weight = 36188.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104655 restraints weight = 14336.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105461 restraints weight = 9512.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105661 restraints weight = 8127.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105833 restraints weight = 7710.937| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2029 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 : 0.533 9.128 22258 Z= 0.285 Chirality : 0.040 0.197 2408 Planarity : 0.003 0.031 2673 Dihedral : 6.736 65.188 2276 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.98 % Allowed : 17.01 % Favored : 80.01 % 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: 1.48 (0.21), residues: 1842 helix: 1.76 (0.15), residues: 1260 sheet: 1.84 (0.52), residues: 96 loop : -1.31 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 309 TYR 0.015 0.001 TYR E 332 PHE 0.029 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/Z covalent geometry : bond 0.00255 / 0.12 (16473) covalent geometry : angle 0.53251 / 0.29 (22222) SS BOND : bond 0.00212 / 0.14 ( 18) SS BOND : angle 0.54421 / 0.37 ( 36) hydrogen bonds : bond 0.03915 / 2.57 ( 1005) hydrogen bonds : angle 3.64765 / 2.59 ( 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 260 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8057 (tmt-80) cc_final: 0.7776 (tpt170) REVERT: B 325 TYR cc_start: 0.8823 (t80) cc_final: 0.8549 (t80) REVERT: C 161 LEU cc_start: 0.8815 (mm) cc_final: 0.8528 (mm) REVERT: D 161 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7620 (pp) REVERT: D 280 CYS cc_start: 0.8767 (m) cc_final: 0.8557 (m) REVERT: E 162 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8611 (mmtm) REVERT: E 168 TRP cc_start: 0.7298 (t60) cc_final: 0.6864 (t60) REVERT: E 255 GLU cc_start: 0.8320 (tp30) cc_final: 0.7986 (tp30) REVERT: E 399 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7823 (mm-30) REVERT: F 249 LYS cc_start: 0.9174 (tptt) cc_final: 0.8627 (pttt) REVERT: F 380 ASP cc_start: 0.8092 (t70) cc_final: 0.7589 (t0) REVERT: F 381 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8155 (mm-40) outliers start: 52 outliers final: 41 residues processed: 234 average time/residue: 0.1078 time to fit residues: 39.3989 Evaluate side-chains 223 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 47 VAL Chi-restraints excluded: chain D residue 104 HIS 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 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 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 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: 0.0020 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.130056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103940 restraints weight = 35579.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105285 restraints weight = 14284.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106776 restraints weight = 8683.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106834 restraints weight = 6640.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107137 restraints weight = 6235.319| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16491 Z= 0.112 Angle : 0.534 9.332 22258 Z= 0.284 Chirality : 0.040 0.204 2408 Planarity : 0.003 0.031 2673 Dihedral : 6.413 64.346 2276 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.81 % Allowed : 18.04 % Favored : 79.15 % 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: 1.54 (0.21), residues: 1842 helix: 1.81 (0.15), residues: 1260 sheet: 1.96 (0.51), residues: 96 loop : -1.31 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.012 0.001 TYR E 332 PHE 0.043 0.001 PHE F 244 TRP 0.019 0.001 TRP C 342 HIS 0.014 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16473) covalent geometry : angle 0.53396 / 0.28 (22222) SS BOND : bond 0.00197 / 0.14 ( 18) SS BOND : angle 0.51278 / 0.35 ( 36) hydrogen bonds : bond 0.03795 / 2.49 ( 1005) hydrogen bonds : angle 3.61043 / 2.56 ( 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 253 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8125 (tmt-80) cc_final: 0.7803 (tpt170) REVERT: B 325 TYR cc_start: 0.8800 (t80) cc_final: 0.8498 (t80) REVERT: C 161 LEU cc_start: 0.8809 (mm) cc_final: 0.8525 (mm) REVERT: D 161 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7611 (pp) REVERT: D 280 CYS cc_start: 0.8766 (m) cc_final: 0.8522 (m) REVERT: D 353 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5535 (t80) REVERT: E 18 ARG cc_start: 0.7876 (ptp-170) cc_final: 0.7430 (ptp90) REVERT: E 162 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8598 (mmtm) REVERT: E 168 TRP cc_start: 0.7265 (t60) cc_final: 0.6792 (t60) REVERT: E 255 GLU cc_start: 0.8257 (tp30) cc_final: 0.7897 (tp30) REVERT: E 399 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7911 (mm-30) REVERT: F 249 LYS cc_start: 0.9179 (tptt) cc_final: 0.8587 (pttt) REVERT: F 380 ASP cc_start: 0.8019 (t70) cc_final: 0.7512 (t0) REVERT: F 381 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8196 (mm-40) outliers start: 49 outliers final: 40 residues processed: 232 average time/residue: 0.1141 time to fit residues: 41.3680 Evaluate side-chains 230 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 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 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 330 ILE 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: 2.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 288 ASN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099838 restraints weight = 36660.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102520 restraints weight = 15717.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103975 restraints weight = 8450.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103999 restraints weight = 7092.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104105 restraints weight = 6239.371| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2159 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= 0.147 Angle : 0.562 8.866 22258 Z= 0.300 Chirality : 0.041 0.191 2408 Planarity : 0.003 0.030 2673 Dihedral : 6.435 63.795 2276 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.15 % Allowed : 18.67 % Favored : 78.18 % 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: 1.55 (0.21), residues: 1842 helix: 1.81 (0.15), residues: 1260 sheet: 1.96 (0.50), residues: 96 loop : -1.28 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 357 TYR 0.013 0.001 TYR B 332 PHE 0.037 0.001 PHE F 244 TRP 0.016 0.001 TRP C 342 HIS 0.011 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16473) covalent geometry : angle 0.56233 / 0.30 (22222) SS BOND : bond 0.00264 / 0.17 ( 18) SS BOND : angle 0.63758 / 0.43 ( 36) hydrogen bonds : bond 0.04128 / 2.71 ( 1005) hydrogen bonds : angle 3.67874 / 2.62 ( 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 241 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8234 (tmt-80) cc_final: 0.7913 (tpt170) REVERT: B 288 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8719 (t0) REVERT: B 325 TYR cc_start: 0.8845 (t80) cc_final: 0.8580 (t80) REVERT: C 161 LEU cc_start: 0.8820 (mm) cc_final: 0.8538 (mm) REVERT: C 330 ILE cc_start: 0.9479 (mm) cc_final: 0.9248 (tt) REVERT: D 161 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7682 (pp) REVERT: D 280 CYS cc_start: 0.8748 (m) cc_final: 0.8490 (m) REVERT: D 353 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.5244 (t80) REVERT: E 18 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7382 (ptp90) REVERT: E 162 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8596 (mmtm) REVERT: E 168 TRP cc_start: 0.7401 (t60) cc_final: 0.6850 (t60) REVERT: E 255 GLU cc_start: 0.8266 (tp30) cc_final: 0.8062 (tp30) REVERT: E 399 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7929 (mm-30) REVERT: F 249 LYS cc_start: 0.9184 (tptt) cc_final: 0.8649 (pptt) REVERT: F 381 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8162 (mm-40) outliers start: 55 outliers final: 44 residues processed: 221 average time/residue: 0.1093 time to fit residues: 37.2919 Evaluate side-chains 221 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 10.0000 chunk 77 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS E 155 HIS E 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.101611 restraints weight = 36176.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104946 restraints weight = 16419.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106040 restraints weight = 8502.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106336 restraints weight = 7143.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106340 restraints weight = 6360.155| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16491 Z= 0.117 Angle : 0.556 8.492 22258 Z= 0.293 Chirality : 0.041 0.259 2408 Planarity : 0.003 0.031 2673 Dihedral : 6.250 63.540 2276 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.92 % Allowed : 18.79 % Favored : 78.29 % 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: 1.59 (0.21), residues: 1842 helix: 1.84 (0.15), residues: 1260 sheet: 1.98 (0.51), residues: 96 loop : -1.27 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.011 0.001 TYR B 332 PHE 0.033 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.013 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16473) covalent geometry : angle 0.55558 / 0.29 (22222) SS BOND : bond 0.00210 / 0.14 ( 18) SS BOND : angle 0.53761 / 0.36 ( 36) hydrogen bonds : bond 0.03888 / 2.56 ( 1005) hydrogen bonds : angle 3.63573 / 2.59 ( 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 242 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8276 (tmt-80) cc_final: 0.7937 (tpt170) REVERT: B 143 TRP cc_start: 0.8546 (t60) cc_final: 0.8182 (t60) REVERT: B 325 TYR cc_start: 0.8802 (t80) cc_final: 0.8505 (t80) REVERT: C 161 LEU cc_start: 0.8828 (mm) cc_final: 0.8562 (mm) REVERT: C 330 ILE cc_start: 0.9465 (mm) cc_final: 0.9264 (tt) REVERT: D 161 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7811 (pp) REVERT: D 280 CYS cc_start: 0.8727 (m) cc_final: 0.8463 (m) REVERT: D 353 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.5162 (t80) REVERT: E 18 ARG cc_start: 0.7867 (ptp-170) cc_final: 0.7353 (ptp90) REVERT: E 162 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8619 (mmtm) REVERT: E 168 TRP cc_start: 0.7379 (t60) cc_final: 0.6871 (t60) REVERT: E 255 GLU cc_start: 0.8295 (tp30) cc_final: 0.8095 (tp30) REVERT: E 288 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8789 (m-40) REVERT: E 399 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7965 (mm-30) REVERT: F 249 LYS cc_start: 0.9181 (tptt) cc_final: 0.8592 (pttt) outliers start: 51 outliers final: 44 residues processed: 221 average time/residue: 0.1021 time to fit residues: 34.7354 Evaluate side-chains 229 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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 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 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 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU 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 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 132 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 150 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3867 r_free = 0.3867 target = 0.129347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102078 restraints weight = 35893.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105369 restraints weight = 16697.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106240 restraints weight = 8598.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106572 restraints weight = 7128.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106622 restraints weight = 6573.577| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16491 Z= 0.117 Angle : 0.557 9.715 22258 Z= 0.294 Chirality : 0.040 0.252 2408 Planarity : 0.003 0.031 2673 Dihedral : 6.177 63.059 2276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.69 % Allowed : 19.24 % Favored : 78.06 % 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: 1.63 (0.21), residues: 1842 helix: 1.85 (0.15), residues: 1260 sheet: 2.08 (0.52), residues: 96 loop : -1.25 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.034 0.001 TYR D 325 PHE 0.031 0.001 PHE F 244 TRP 0.015 0.001 TRP C 143 HIS 0.016 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (16473) covalent geometry : angle 0.55735 / 0.29 (22222) SS BOND : bond 0.00205 / 0.14 ( 18) SS BOND : angle 0.52700 / 0.35 ( 36) hydrogen bonds : bond 0.03825 / 2.52 ( 1005) hydrogen bonds : angle 3.62785 / 2.58 ( 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 244 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8266 (tmt-80) cc_final: 0.7932 (tpt170) REVERT: B 143 TRP cc_start: 0.8507 (t60) cc_final: 0.8200 (t60) REVERT: B 325 TYR cc_start: 0.8790 (t80) cc_final: 0.8497 (t80) REVERT: C 161 LEU cc_start: 0.8830 (mm) cc_final: 0.8570 (mm) REVERT: C 245 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8865 (mm-30) REVERT: D 161 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7782 (pp) REVERT: D 280 CYS cc_start: 0.8715 (m) cc_final: 0.8458 (m) REVERT: D 353 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5215 (t80) REVERT: E 18 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7466 (ptp90) REVERT: E 162 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8618 (mmtm) REVERT: E 168 TRP cc_start: 0.7403 (t60) cc_final: 0.6888 (t60) REVERT: E 288 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8765 (m-40) REVERT: E 399 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 249 LYS cc_start: 0.9178 (tptt) cc_final: 0.8664 (pptt) outliers start: 47 outliers final: 43 residues processed: 226 average time/residue: 0.1063 time to fit residues: 37.1646 Evaluate side-chains 231 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 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 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 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 40 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 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU 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 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: 0.9980 chunk 185 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN B 253 HIS 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 = 0.3855 r_free = 0.3855 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101044 restraints weight = 36064.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104342 restraints weight = 16984.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105668 restraints weight = 8710.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105937 restraints weight = 7362.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106030 restraints weight = 6269.873| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2335 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= 0.127 Angle : 0.570 11.261 22258 Z= 0.300 Chirality : 0.041 0.295 2408 Planarity : 0.003 0.031 2673 Dihedral : 6.135 62.987 2276 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.92 % Allowed : 19.30 % Favored : 77.78 % 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: 1.63 (0.21), residues: 1842 helix: 1.85 (0.15), residues: 1260 sheet: 2.11 (0.52), residues: 96 loop : -1.23 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.031 0.001 TYR D 325 PHE 0.043 0.001 PHE F 244 TRP 0.023 0.001 TRP C 342 HIS 0.013 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16473) covalent geometry : angle 0.57021 / 0.30 (22222) SS BOND : bond 0.00221 / 0.15 ( 18) SS BOND : angle 0.55504 / 0.37 ( 36) hydrogen bonds : bond 0.03923 / 2.58 ( 1005) hydrogen bonds : angle 3.65418 / 2.60 ( 2949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.82 seconds wall clock time: 41 minutes 3.96 seconds (2463.96 seconds total)