Starting phenix.real_space_refine on Fri Jul 3 21:57:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m17_23614/07_2026/7m17_23614.cif" } resolution = 3.65 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 109 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: 3.37, per 1000 atoms: 0.21 Number of scatterers: 16039 At special positions: 0 Unit cell: (112.563, 100.056, 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=2.03 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=2.02 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: 1.08 Conformation dependent library (CDL) restraints added in 500.9 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: 92 helices and 10 sheets defined 75.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.707A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 26 through 49 Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.510A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.716A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 4.485A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.711A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.145A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.678A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.185A 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: 4.322A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.806A 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: 3.947A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 120 through 146 removed outlier: 3.809A pdb=" N PHE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 5.100A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.569A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.741A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 removed outlier: 3.683A pdb=" N GLU B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 286 removed outlier: 3.986A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.260A 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: 3.861A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.728A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.300A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 394 removed outlier: 3.518A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.853A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Proline residue: C 22 - end of helix Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.661A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.742A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 3.584A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.597A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 removed outlier: 4.094A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.597A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.729A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.198A 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 346 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.587A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 3.691A 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 383 through 389 removed outlier: 4.547A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.854A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.642A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.580A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 124 through 146 removed outlier: 4.464A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 3.876A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.040A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 256 removed outlier: 3.610A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.705A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.302A 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 347 removed outlier: 4.199A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.677A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.559A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 25 Processing helix chain 'E' and resid 26 through 49 Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.616A pdb=" N VAL E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.883A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.936A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.684A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 removed outlier: 4.374A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.667A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 3.836A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.215A 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 347 removed outlier: 4.021A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.112A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.174A 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 390 through 394 Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 16 through 22 removed outlier: 3.703A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Proline residue: F 22 - end of helix Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.846A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 removed outlier: 3.589A pdb=" N ARG F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.799A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.438A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.459A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 3.762A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.527A pdb=" N GLU F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 286 removed outlier: 3.620A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.207A 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: 3.932A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 4.111A 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 390 removed outlier: 4.478A 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 removed outlier: 3.856A pdb=" N CYS A 295 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.942A pdb=" N VAL B 293 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.518A pdb=" N ILE C 53 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 293 " --> pdb=" O CYS C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.548A pdb=" N ILE D 53 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 293 " --> pdb=" O CYS D 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.502A pdb=" N CYS E 295 " --> pdb=" O TYR E 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 56 996 hydrogen bonds defined for protein. 2901 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: 2.55 Time building geometry restraints manager: 1.57 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: 9003 1.57 - 1.70: 8 1.70 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE D 902 " pdb=" C19 PEE D 902 " ideal model delta sigma weight residual 1.523 1.339 0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C18 PEE A 901 " pdb=" C19 PEE A 901 " 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 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 8.37e+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 8.35e+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 8.34e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 21756 2.82 - 5.65: 348 5.65 - 8.47: 60 8.47 - 11.30: 35 11.30 - 14.12: 23 Bond angle restraints: 22222 Sorted by residual: angle pdb=" CA PRO E 15 " pdb=" N PRO E 15 " pdb=" CD PRO E 15 " ideal model delta sigma weight residual 112.00 102.61 9.39 1.40e+00 5.10e-01 4.50e+01 angle pdb=" C THR A 48 " pdb=" N GLN A 49 " pdb=" CA GLN A 49 " ideal model delta sigma weight residual 121.90 114.40 7.50 1.26e+00 6.30e-01 3.54e+01 angle pdb=" CA PRO F 366 " pdb=" N PRO F 366 " pdb=" CD PRO F 366 " ideal model delta sigma weight residual 112.00 104.11 7.89 1.40e+00 5.10e-01 3.18e+01 angle pdb=" C THR D 48 " pdb=" N GLN D 49 " pdb=" CA GLN D 49 " ideal model delta sigma weight residual 121.90 114.91 6.99 1.26e+00 6.30e-01 3.08e+01 angle pdb=" C CYS C 280 " pdb=" N TYR C 281 " pdb=" CA TYR C 281 " ideal model delta sigma weight residual 122.09 113.63 8.46 1.79e+00 3.12e-01 2.23e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 9178 27.09 - 54.19: 532 54.19 - 81.28: 26 81.28 - 108.37: 10 108.37 - 135.47: 6 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 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR F 264 " pdb=" C TYR F 264 " pdb=" N MET F 265 " pdb=" CA MET F 265 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA TYR E 264 " pdb=" C TYR E 264 " pdb=" N MET E 265 " pdb=" CA MET E 265 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 9749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1915 0.062 - 0.124: 441 0.124 - 0.187: 47 0.187 - 0.249: 4 0.249 - 0.311: 1 Chirality restraints: 2408 Sorted by residual: 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 2.69 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE C 365 " pdb=" CA ILE C 365 " pdb=" CG1 ILE C 365 " pdb=" CG2 ILE C 365 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO F 366 " pdb=" N PRO F 366 " pdb=" C PRO F 366 " pdb=" CB PRO F 366 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 325 " 0.012 2.00e-02 2.50e+03 1.86e-02 6.93e+00 pdb=" CG TYR A 325 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 325 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 325 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 325 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 325 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 325 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 325 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 275 " -0.013 2.00e-02 2.50e+03 1.87e-02 6.10e+00 pdb=" CG PHE A 275 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 275 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 275 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 275 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 275 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 275 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 143 " -0.019 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP B 143 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 143 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 143 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 143 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 143 " 0.000 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2826 2.77 - 3.30: 14912 3.30 - 3.83: 26463 3.83 - 4.37: 28471 4.37 - 4.90: 50338 Nonbonded interactions: 123010 Sorted by model distance: nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP F 50 " pdb=" OH TYR F 114 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP D 50 " pdb=" OH TYR D 114 " model vdw 2.252 3.040 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.257 3.040 ... (remaining 123005 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: 4.240 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.184 16491 Z= 0.472 Angle : 1.024 14.123 22258 Z= 0.503 Chirality : 0.052 0.311 2408 Planarity : 0.005 0.050 2673 Dihedral : 15.789 135.465 6038 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.06 (0.19), residues: 1842 helix: -0.22 (0.14), residues: 1254 sheet: -0.33 (0.52), residues: 96 loop : -1.75 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.043 0.002 TYR A 325 PHE 0.042 0.002 PHE A 275 TRP 0.041 0.002 TRP B 143 HIS 0.014 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00969 / 0.47 (16473) covalent geometry : angle 1.02388 / 0.50 (22222) SS BOND : bond 0.00330 / 0.21 ( 18) SS BOND : angle 0.92233 / 0.59 ( 36) hydrogen bonds : bond 0.12340 / 8.21 ( 996) hydrogen bonds : angle 5.32368 / 3.74 ( 2901) *********************** 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 246 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8551 (mmpt) cc_final: 0.7935 (mtmm) REVERT: A 288 ASN cc_start: 0.8698 (t0) cc_final: 0.8186 (t0) REVERT: B 250 PHE cc_start: 0.7795 (t80) cc_final: 0.7214 (t80) REVERT: B 280 CYS cc_start: 0.8324 (t) cc_final: 0.8120 (t) REVERT: B 292 ASP cc_start: 0.8032 (m-30) cc_final: 0.7818 (p0) REVERT: C 280 CYS cc_start: 0.8909 (m) cc_final: 0.8576 (m) REVERT: D 157 VAL cc_start: 0.8825 (p) cc_final: 0.8596 (p) REVERT: D 280 CYS cc_start: 0.8307 (t) cc_final: 0.8047 (t) REVERT: E 168 TRP cc_start: 0.7921 (t60) cc_final: 0.7685 (t-100) REVERT: E 236 GLU cc_start: 0.8205 (tp30) cc_final: 0.7222 (pt0) REVERT: F 29 ASP cc_start: 0.8026 (t70) cc_final: 0.7608 (p0) REVERT: F 404 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7628 (tp40) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.0943 time to fit residues: 37.2014 Evaluate side-chains 183 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN A 155 HIS A 253 HIS B 155 HIS C 105 GLN C 155 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 377 HIS D 105 GLN D 288 ASN D 406 ASN E 105 GLN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091051 restraints weight = 36773.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093736 restraints weight = 17153.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095426 restraints weight = 10660.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096462 restraints weight = 8040.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096975 restraints weight = 6864.865| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16491 Z= 0.138 Angle : 0.569 11.576 22258 Z= 0.305 Chirality : 0.041 0.162 2408 Planarity : 0.004 0.041 2673 Dihedral : 9.825 105.395 2276 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 9.45 % Favored : 89.00 % 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: -0.02 (0.20), residues: 1842 helix: 0.73 (0.15), residues: 1284 sheet: -0.11 (0.71), residues: 60 loop : -1.86 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.029 0.001 TYR C 281 PHE 0.015 0.001 PHE D 275 TRP 0.025 0.001 TRP B 168 HIS 0.009 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16473) covalent geometry : angle 0.56888 / 0.31 (22222) SS BOND : bond 0.00229 / 0.14 ( 18) SS BOND : angle 0.71159 / 0.45 ( 36) hydrogen bonds : bond 0.04603 / 3.02 ( 996) hydrogen bonds : angle 4.00688 / 2.81 ( 2901) *********************** 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 231 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9197 (tp) cc_final: 0.8992 (tt) REVERT: A 162 LYS cc_start: 0.8421 (mmpt) cc_final: 0.7805 (mtmm) REVERT: B 280 CYS cc_start: 0.8526 (t) cc_final: 0.8258 (t) REVERT: B 292 ASP cc_start: 0.8377 (m-30) cc_final: 0.8016 (p0) REVERT: C 45 LEU cc_start: 0.9529 (tt) cc_final: 0.9166 (tp) REVERT: C 49 GLN cc_start: 0.7978 (mp10) cc_final: 0.7765 (mp10) REVERT: D 280 CYS cc_start: 0.8351 (t) cc_final: 0.8140 (t) REVERT: D 288 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9096 (m-40) REVERT: E 29 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8084 (t70) REVERT: E 143 TRP cc_start: 0.8533 (t60) cc_final: 0.8303 (t60) REVERT: E 245 GLU cc_start: 0.8178 (tp30) cc_final: 0.7960 (tp30) REVERT: F 29 ASP cc_start: 0.8107 (t70) cc_final: 0.7578 (t0) REVERT: F 239 GLN cc_start: 0.7530 (mp10) cc_final: 0.7241 (pm20) REVERT: F 404 GLN cc_start: 0.7512 (tp-100) cc_final: 0.7307 (tp-100) outliers start: 27 outliers final: 16 residues processed: 221 average time/residue: 0.0917 time to fit residues: 33.0164 Evaluate side-chains 196 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 326 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 182 optimal weight: 0.0010 chunk 159 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 406 ASN B 155 HIS B 253 HIS C 155 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094418 restraints weight = 37201.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096628 restraints weight = 18282.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099285 restraints weight = 10442.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099283 restraints weight = 7607.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099202 restraints weight = 6982.875| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16491 Z= 0.112 Angle : 0.523 9.997 22258 Z= 0.280 Chirality : 0.040 0.152 2408 Planarity : 0.003 0.040 2673 Dihedral : 8.137 75.816 2276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.55 % Allowed : 12.31 % Favored : 86.14 % 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: 0.60 (0.20), residues: 1842 helix: 1.14 (0.15), residues: 1284 sheet: 0.29 (0.53), residues: 96 loop : -1.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 309 TYR 0.021 0.001 TYR E 325 PHE 0.011 0.001 PHE F 125 TRP 0.023 0.001 TRP A 168 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (16473) covalent geometry : angle 0.52299 / 0.28 (22222) SS BOND : bond 0.00192 / 0.12 ( 18) SS BOND : angle 0.57754 / 0.36 ( 36) hydrogen bonds : bond 0.04053 / 2.66 ( 996) hydrogen bonds : angle 3.73669 / 2.62 ( 2901) *********************** 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 236 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9206 (tp) cc_final: 0.8975 (tt) REVERT: A 48 THR cc_start: 0.8742 (t) cc_final: 0.7788 (t) REVERT: A 162 LYS cc_start: 0.8459 (mmpt) cc_final: 0.7897 (mtmm) REVERT: A 168 TRP cc_start: 0.7686 (t-100) cc_final: 0.7304 (t-100) REVERT: A 343 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: B 280 CYS cc_start: 0.8575 (t) cc_final: 0.8307 (t) REVERT: B 292 ASP cc_start: 0.8391 (m-30) cc_final: 0.8039 (p0) REVERT: C 17 TYR cc_start: 0.7423 (m-80) cc_final: 0.7188 (m-80) REVERT: C 45 LEU cc_start: 0.9500 (tt) cc_final: 0.9291 (tp) REVERT: C 395 SER cc_start: 0.7953 (m) cc_final: 0.7336 (t) REVERT: E 29 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (t70) REVERT: E 245 GLU cc_start: 0.8184 (tp30) cc_final: 0.7973 (tp30) REVERT: F 29 ASP cc_start: 0.8188 (t70) cc_final: 0.7653 (t0) REVERT: F 115 GLU cc_start: 0.8035 (tt0) cc_final: 0.7694 (tt0) REVERT: F 337 MET cc_start: 0.8631 (mtt) cc_final: 0.7845 (tmm) outliers start: 27 outliers final: 17 residues processed: 226 average time/residue: 0.0971 time to fit residues: 34.9366 Evaluate side-chains 196 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 182 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS B 155 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 288 ASN ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 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 = 0.3779 r_free = 0.3779 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.094801 restraints weight = 36896.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097342 restraints weight = 17725.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099889 restraints weight = 9777.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099838 restraints weight = 7405.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099805 restraints weight = 6718.756| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1766 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= 0.120 Angle : 0.533 11.020 22258 Z= 0.283 Chirality : 0.040 0.185 2408 Planarity : 0.003 0.039 2673 Dihedral : 7.392 58.713 2276 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.29 % Allowed : 13.40 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1842 helix: 1.35 (0.15), residues: 1284 sheet: 0.46 (0.52), residues: 96 loop : -1.51 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.023 0.001 TYR F 325 PHE 0.015 0.001 PHE B 144 TRP 0.020 0.001 TRP B 143 HIS 0.010 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16473) covalent geometry : angle 0.53305 / 0.28 (22222) SS BOND : bond 0.00191 / 0.12 ( 18) SS BOND : angle 0.58733 / 0.36 ( 36) hydrogen bonds : bond 0.03959 / 2.60 ( 996) hydrogen bonds : angle 3.63405 / 2.55 ( 2901) *********************** 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 237 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9231 (tp) cc_final: 0.8981 (tt) REVERT: A 162 LYS cc_start: 0.8520 (mmpt) cc_final: 0.7968 (mtmm) REVERT: A 357 ARG cc_start: 0.7085 (ptp-170) cc_final: 0.6740 (ptp-170) REVERT: B 292 ASP cc_start: 0.8348 (m-30) cc_final: 0.7997 (p0) REVERT: C 17 TYR cc_start: 0.7427 (m-80) cc_final: 0.7161 (m-80) REVERT: C 29 ASP cc_start: 0.8753 (t0) cc_final: 0.8505 (t0) REVERT: C 45 LEU cc_start: 0.9539 (tt) cc_final: 0.9279 (tp) REVERT: C 280 CYS cc_start: 0.8961 (m) cc_final: 0.8526 (m) REVERT: C 395 SER cc_start: 0.7931 (m) cc_final: 0.7339 (t) REVERT: D 328 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7669 (tt) REVERT: D 352 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8754 (t) REVERT: F 115 GLU cc_start: 0.7899 (tt0) cc_final: 0.7627 (tt0) REVERT: F 337 MET cc_start: 0.8624 (mtt) cc_final: 0.7840 (tmm) outliers start: 40 outliers final: 26 residues processed: 224 average time/residue: 0.0955 time to fit residues: 34.6680 Evaluate side-chains 208 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN 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 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 326 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 406 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093189 restraints weight = 37151.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095947 restraints weight = 17130.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097736 restraints weight = 10554.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098789 restraints weight = 7904.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099292 restraints weight = 6727.323| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1888 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 : 0.536 13.099 22258 Z= 0.281 Chirality : 0.040 0.154 2408 Planarity : 0.003 0.039 2673 Dihedral : 7.126 59.455 2276 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.52 % Allowed : 14.72 % Favored : 82.76 % 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: 1.04 (0.21), residues: 1842 helix: 1.46 (0.15), residues: 1284 sheet: 0.54 (0.51), residues: 96 loop : -1.45 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.023 0.001 TYR E 325 PHE 0.020 0.001 PHE A 144 TRP 0.031 0.001 TRP A 168 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16473) covalent geometry : angle 0.53629 / 0.28 (22222) SS BOND : bond 0.00198 / 0.13 ( 18) SS BOND : angle 0.57400 / 0.35 ( 36) hydrogen bonds : bond 0.03863 / 2.54 ( 996) hydrogen bonds : angle 3.60566 / 2.53 ( 2901) *********************** 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 232 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9198 (tp) cc_final: 0.8949 (tt) REVERT: A 162 LYS cc_start: 0.8549 (mmpt) cc_final: 0.7996 (mtmm) REVERT: A 357 ARG cc_start: 0.7099 (ptp-170) cc_final: 0.6751 (ptp-170) REVERT: B 292 ASP cc_start: 0.8455 (m-30) cc_final: 0.8021 (p0) REVERT: C 17 TYR cc_start: 0.7363 (m-80) cc_final: 0.7129 (m-80) REVERT: C 29 ASP cc_start: 0.8698 (t0) cc_final: 0.8246 (t0) REVERT: C 280 CYS cc_start: 0.8978 (m) cc_final: 0.8552 (m) REVERT: D 328 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (tt) REVERT: D 352 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8778 (t) REVERT: F 337 MET cc_start: 0.8681 (mtt) cc_final: 0.7840 (tmm) outliers start: 44 outliers final: 31 residues processed: 217 average time/residue: 0.0933 time to fit residues: 32.9090 Evaluate side-chains 205 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089721 restraints weight = 37571.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091714 restraints weight = 18533.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093329 restraints weight = 10758.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093472 restraints weight = 8929.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093440 restraints weight = 7837.543| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16491 Z= 0.197 Angle : 0.606 10.906 22258 Z= 0.319 Chirality : 0.042 0.150 2408 Planarity : 0.003 0.040 2673 Dihedral : 7.220 57.279 2276 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.92 % Allowed : 16.27 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1842 helix: 1.48 (0.15), residues: 1272 sheet: 0.52 (0.50), residues: 96 loop : -1.69 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.031 0.001 TYR F 325 PHE 0.017 0.002 PHE B 372 TRP 0.032 0.001 TRP A 168 HIS 0.010 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (16473) covalent geometry : angle 0.60524 / 0.32 (22222) SS BOND : bond 0.00329 / 0.21 ( 18) SS BOND : angle 0.78003 / 0.49 ( 36) hydrogen bonds : bond 0.04520 / 2.98 ( 996) hydrogen bonds : angle 3.81483 / 2.68 ( 2901) *********************** 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 232 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8526 (mmpt) cc_final: 0.7959 (mtmm) REVERT: B 292 ASP cc_start: 0.8362 (m-30) cc_final: 0.7953 (p0) REVERT: C 17 TYR cc_start: 0.7566 (m-80) cc_final: 0.7233 (m-80) REVERT: C 29 ASP cc_start: 0.8720 (t0) cc_final: 0.8281 (t0) REVERT: C 280 CYS cc_start: 0.8883 (m) cc_final: 0.8318 (m) REVERT: D 52 MET cc_start: 0.7424 (ptt) cc_final: 0.7102 (ptt) REVERT: D 352 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8863 (t) REVERT: E 236 GLU cc_start: 0.8110 (tp30) cc_final: 0.7141 (mp0) REVERT: F 239 GLN cc_start: 0.7370 (mp10) cc_final: 0.7086 (pm20) outliers start: 51 outliers final: 33 residues processed: 213 average time/residue: 0.0919 time to fit residues: 31.8663 Evaluate side-chains 200 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 400 ASN 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 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 406 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093706 restraints weight = 36512.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096306 restraints weight = 17450.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098523 restraints weight = 9733.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098521 restraints weight = 7692.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098521 restraints weight = 6968.072| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16491 Z= 0.126 Angle : 0.559 11.550 22258 Z= 0.295 Chirality : 0.040 0.146 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.949 58.151 2276 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.75 % Allowed : 17.24 % 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: 1.11 (0.21), residues: 1842 helix: 1.58 (0.15), residues: 1272 sheet: 0.66 (0.50), residues: 96 loop : -1.60 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.026 0.001 TYR E 325 PHE 0.013 0.001 PHE B 144 TRP 0.025 0.001 TRP A 168 HIS 0.011 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16473) covalent geometry : angle 0.55940 / 0.29 (22222) SS BOND : bond 0.00204 / 0.13 ( 18) SS BOND : angle 0.59957 / 0.37 ( 36) hydrogen bonds : bond 0.04100 / 2.71 ( 996) hydrogen bonds : angle 3.64080 / 2.56 ( 2901) *********************** 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 228 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8546 (mmpt) cc_final: 0.7964 (mtmm) REVERT: A 343 MET cc_start: 0.8405 (ttt) cc_final: 0.8078 (ttt) REVERT: A 357 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6642 (ptp-110) REVERT: B 292 ASP cc_start: 0.8369 (m-30) cc_final: 0.8029 (p0) REVERT: C 17 TYR cc_start: 0.7472 (m-80) cc_final: 0.7233 (m-80) REVERT: C 29 ASP cc_start: 0.8639 (t0) cc_final: 0.8224 (t0) REVERT: C 280 CYS cc_start: 0.8853 (m) cc_final: 0.8305 (m) REVERT: D 352 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8893 (t) REVERT: E 35 MET cc_start: 0.8425 (mtp) cc_final: 0.8218 (mtp) REVERT: E 236 GLU cc_start: 0.8088 (tp30) cc_final: 0.7238 (mp0) REVERT: F 110 ASP cc_start: 0.7995 (m-30) cc_final: 0.7774 (m-30) outliers start: 48 outliers final: 34 residues processed: 214 average time/residue: 0.0899 time to fit residues: 31.4294 Evaluate side-chains 207 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN 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 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 326 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 0.0070 chunk 164 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093820 restraints weight = 36999.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096460 restraints weight = 17305.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098865 restraints weight = 9555.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098802 restraints weight = 7385.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098785 restraints weight = 6766.022| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16491 Z= 0.118 Angle : 0.563 11.940 22258 Z= 0.293 Chirality : 0.040 0.156 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.679 58.967 2276 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.63 % Allowed : 17.64 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1842 helix: 1.64 (0.15), residues: 1272 sheet: 0.79 (0.51), residues: 96 loop : -1.58 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 403 TYR 0.028 0.001 TYR E 325 PHE 0.013 0.001 PHE F 125 TRP 0.023 0.001 TRP B 168 HIS 0.013 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16473) covalent geometry : angle 0.56342 / 0.29 (22222) SS BOND : bond 0.00187 / 0.12 ( 18) SS BOND : angle 0.54664 / 0.34 ( 36) hydrogen bonds : bond 0.03896 / 2.58 ( 996) hydrogen bonds : angle 3.59484 / 2.53 ( 2901) *********************** 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 233 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8515 (mmpt) cc_final: 0.7947 (mtmm) REVERT: A 357 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6350 (ptp-110) REVERT: B 292 ASP cc_start: 0.8456 (m-30) cc_final: 0.8017 (p0) REVERT: C 17 TYR cc_start: 0.7382 (m-80) cc_final: 0.7103 (m-80) REVERT: C 29 ASP cc_start: 0.8667 (t0) cc_final: 0.8247 (t0) REVERT: C 280 CYS cc_start: 0.8925 (m) cc_final: 0.8482 (m) REVERT: D 352 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8882 (t) REVERT: E 35 MET cc_start: 0.8434 (mtp) cc_final: 0.8196 (mtp) REVERT: E 236 GLU cc_start: 0.8031 (tp30) cc_final: 0.7210 (mp0) REVERT: F 104 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8218 (t70) REVERT: F 110 ASP cc_start: 0.8039 (m-30) cc_final: 0.7819 (m-30) outliers start: 46 outliers final: 36 residues processed: 219 average time/residue: 0.0956 time to fit residues: 34.3636 Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 LYS 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 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 326 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS A 406 ASN B 116 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 400 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 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 = 0.3757 r_free = 0.3757 target = 0.124711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094100 restraints weight = 36879.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096590 restraints weight = 17793.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099086 restraints weight = 9862.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099093 restraints weight = 7552.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099066 restraints weight = 6731.186| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16491 Z= 0.143 Angle : 0.587 12.492 22258 Z= 0.304 Chirality : 0.041 0.173 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.638 59.192 2276 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.81 % Allowed : 17.81 % Favored : 79.38 % 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: 1.20 (0.21), residues: 1842 helix: 1.64 (0.15), residues: 1272 sheet: 0.85 (0.52), residues: 96 loop : -1.56 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 251 TYR 0.025 0.001 TYR E 325 PHE 0.016 0.001 PHE B 144 TRP 0.024 0.001 TRP B 168 HIS 0.013 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16473) covalent geometry : angle 0.58690 / 0.30 (22222) SS BOND : bond 0.00233 / 0.15 ( 18) SS BOND : angle 0.60716 / 0.38 ( 36) hydrogen bonds : bond 0.04018 / 2.66 ( 996) hydrogen bonds : angle 3.63479 / 2.56 ( 2901) *********************** 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 229 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8541 (mmpt) cc_final: 0.7963 (mtmm) REVERT: A 357 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6380 (ptp-110) REVERT: B 292 ASP cc_start: 0.8398 (m-30) cc_final: 0.8023 (p0) REVERT: C 17 TYR cc_start: 0.7392 (m-80) cc_final: 0.7089 (m-80) REVERT: C 29 ASP cc_start: 0.8647 (t0) cc_final: 0.8228 (t0) REVERT: C 280 CYS cc_start: 0.8852 (m) cc_final: 0.8297 (m) REVERT: D 352 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8892 (t) REVERT: E 236 GLU cc_start: 0.8041 (tp30) cc_final: 0.7220 (mp0) REVERT: F 104 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8263 (t70) REVERT: F 110 ASP cc_start: 0.7937 (m-30) cc_final: 0.7691 (m-30) outliers start: 49 outliers final: 40 residues processed: 215 average time/residue: 0.0921 time to fit residues: 31.7926 Evaluate side-chains 218 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 400 ASN 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 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 62 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093008 restraints weight = 36685.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095734 restraints weight = 17040.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097516 restraints weight = 10603.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098443 restraints weight = 7984.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099054 restraints weight = 6907.458| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16491 Z= 0.122 Angle : 0.585 12.957 22258 Z= 0.300 Chirality : 0.040 0.202 2408 Planarity : 0.003 0.037 2673 Dihedral : 6.523 59.391 2276 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.63 % Allowed : 18.04 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1842 helix: 1.64 (0.15), residues: 1272 sheet: 0.93 (0.52), residues: 96 loop : -1.51 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.031 0.001 TYR E 325 PHE 0.014 0.001 PHE B 144 TRP 0.025 0.001 TRP A 168 HIS 0.014 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16473) covalent geometry : angle 0.58481 / 0.30 (22222) SS BOND : bond 0.00189 / 0.12 ( 18) SS BOND : angle 0.54588 / 0.34 ( 36) hydrogen bonds : bond 0.03918 / 2.60 ( 996) hydrogen bonds : angle 3.61356 / 2.55 ( 2901) ********************** 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 231 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8531 (mmpt) cc_final: 0.7952 (mtmm) REVERT: A 357 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6369 (ptp-110) REVERT: B 292 ASP cc_start: 0.8477 (m-30) cc_final: 0.8012 (p0) REVERT: C 17 TYR cc_start: 0.7337 (m-80) cc_final: 0.7035 (m-80) REVERT: C 29 ASP cc_start: 0.8661 (t0) cc_final: 0.8342 (t0) REVERT: C 280 CYS cc_start: 0.8888 (m) cc_final: 0.8499 (m) REVERT: D 352 SER cc_start: 0.9127 (OUTLIER) cc_final: 0.8874 (t) REVERT: E 35 MET cc_start: 0.8429 (mtp) cc_final: 0.8219 (mtp) REVERT: E 236 GLU cc_start: 0.8110 (tp30) cc_final: 0.7322 (mp0) REVERT: F 104 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8155 (t70) REVERT: F 110 ASP cc_start: 0.8092 (m-30) cc_final: 0.7848 (m-30) outliers start: 46 outliers final: 38 residues processed: 219 average time/residue: 0.0953 time to fit residues: 33.7966 Evaluate side-chains 222 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 95 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS A 253 HIS A 406 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 400 ASN E 404 GLN ** F 288 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 = 0.3767 r_free = 0.3767 target = 0.124174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093543 restraints weight = 36762.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095825 restraints weight = 17857.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098371 restraints weight = 10203.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098270 restraints weight = 7842.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098251 restraints weight = 7126.722| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2261 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= 0.124 Angle : 0.575 12.987 22258 Z= 0.297 Chirality : 0.040 0.152 2408 Planarity : 0.003 0.037 2673 Dihedral : 6.365 57.128 2276 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.69 % Allowed : 18.04 % Favored : 79.27 % 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: 1.32 (0.21), residues: 1842 helix: 1.70 (0.15), residues: 1266 sheet: 0.98 (0.52), residues: 96 loop : -1.39 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 251 TYR 0.029 0.001 TYR E 325 PHE 0.014 0.001 PHE B 144 TRP 0.027 0.001 TRP A 168 HIS 0.014 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16473) covalent geometry : angle 0.57458 / 0.30 (22222) SS BOND : bond 0.00193 / 0.12 ( 18) SS BOND : angle 0.54837 / 0.34 ( 36) hydrogen bonds : bond 0.03868 / 2.57 ( 996) hydrogen bonds : angle 3.58505 / 2.52 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.82 seconds wall clock time: 38 minutes 28.28 seconds (2308.28 seconds total)