Starting phenix.real_space_refine on Sun Aug 24 02:55:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m17_23614/08_2025/7m17_23614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m17_23614/08_2025/7m17_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_23614/08_2025/7m17_23614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m17_23614/08_2025/7m17_23614.map" model { file = "/net/cci-nas-00/data/ceres_data/7m17_23614/08_2025/7m17_23614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m17_23614/08_2025/7m17_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16039 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'PEE': 3, 'YNJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.35, per 1000 atoms: 0.27 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: 1.34 Conformation dependent library (CDL) restraints added in 737.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 2.13 Time building geometry restraints manager: 1.83 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: 9200 27.09 - 54.19: 532 54.19 - 81.28: 26 81.28 - 108.37: 10 108.37 - 135.47: 6 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 153.41 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 9771 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.730 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 15.768 135.465 6060 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 aren 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 covalent geometry : bond 0.00969 (16473) covalent geometry : angle 1.02388 (22222) SS BOND : bond 0.00330 ( 18) SS BOND : angle 0.92233 ( 36) hydrogen bonds : bond 0.12340 ( 996) hydrogen bonds : angle 5.32368 ( 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 : 0.508 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: 0.7796 (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: 0.0913 time to fit residues: 36.0415 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 : 0.497 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3751 r_free = 0.3751 target = 0.122692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091116 restraints weight = 36938.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093792 restraints weight = 17241.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095493 restraints weight = 10734.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096470 restraints weight = 8104.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097053 restraints weight = 6954.290| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16491 Z= 0.137 Angle : 0.567 11.272 22258 Z= 0.304 Chirality : 0.041 0.166 2408 Planarity : 0.004 0.041 2673 Dihedral : 9.728 104.880 2298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 9.39 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.20), residues: 1842 helix: 0.74 (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 D 309 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 covalent geometry : bond 0.00307 (16473) covalent geometry : angle 0.56658 (22222) SS BOND : bond 0.00230 ( 18) SS BOND : angle 0.71032 ( 36) hydrogen bonds : bond 0.04574 ( 996) hydrogen bonds : angle 3.98478 ( 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 233 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.605 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: 0.8990 (tt) REVERT: A 162 LYS cc_start: 0.8421 (mmpt) cc_final: 0.7805 (mtmm) REVERT: A 369 LYS cc_start: 0.8602 (tppt) cc_final: 0.8395 (tppt) REVERT: B 280 CYS cc_start: 0.8527 (t) cc_final: 0.8262 (t) REVERT: B 292 ASP cc_start: 0.8370 (m-30) cc_final: 0.8014 (p0) REVERT: C 45 LEU cc_start: 0.9530 (tt) cc_final: 0.9167 (tp) REVERT: C 49 GLN cc_start: 0.7969 (mp10) cc_final: 0.7758 (mp10) REVERT: D 280 CYS cc_start: 0.8350 (t) cc_final: 0.8140 (t) REVERT: D 288 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9099 (m-40) REVERT: E 29 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8050 (t70) REVERT: E 143 TRP cc_start: 0.8525 (t60) cc_final: 0.8298 (t60) REVERT: E 245 GLU cc_start: 0.8164 (tp30) cc_final: 0.7956 (tp30) REVERT: F 29 ASP cc_start: 0.8234 (t70) cc_final: 0.7669 (t0) REVERT: F 115 GLU cc_start: 0.8055 (tt0) cc_final: 0.7693 (tt0) REVERT: F 239 GLN cc_start: 0.7539 (mp10) cc_final: 0.7258 (pm20) REVERT: F 404 GLN cc_start: 0.7519 (tp-100) cc_final: 0.7317 (tp-100) outliers start: 27 outliers final: 16 residues processed: 224 average time/residue: 0.0929 time to fit residues: 33.7321 Evaluate side-chains 195 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.6980 chunk 164 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 0.0870 chunk 159 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 406 ASN B 155 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 155 HIS ** C 267 GLN ** 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 = 0.3778 r_free = 0.3778 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094127 restraints weight = 37253.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096505 restraints weight = 18313.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098951 restraints weight = 10295.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099093 restraints weight = 7690.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098964 restraints weight = 6877.673| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16491 Z= 0.113 Angle : 0.524 10.263 22258 Z= 0.280 Chirality : 0.040 0.151 2408 Planarity : 0.003 0.040 2673 Dihedral : 8.110 75.988 2298 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.83 % Allowed : 12.20 % Favored : 85.97 % 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 aren not related in a simple way. whole: 0.61 (0.20), residues: 1842 helix: 1.15 (0.15), residues: 1284 sheet: 0.29 (0.53), residues: 96 loop : -1.62 (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 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00242 (16473) covalent geometry : angle 0.52388 (22222) SS BOND : bond 0.00196 ( 18) SS BOND : angle 0.58831 ( 36) hydrogen bonds : bond 0.04065 ( 996) hydrogen bonds : angle 3.73201 ( 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 235 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.627 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: 0.9208 (tp) cc_final: 0.8981 (tt) REVERT: A 48 THR cc_start: 0.8749 (t) cc_final: 0.7787 (t) REVERT: A 162 LYS cc_start: 0.8461 (mmpt) cc_final: 0.7898 (mtmm) REVERT: A 168 TRP cc_start: 0.7680 (t-100) cc_final: 0.7304 (t-100) REVERT: A 343 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8177 (ttt) REVERT: B 292 ASP cc_start: 0.8397 (m-30) cc_final: 0.8039 (p0) REVERT: C 17 TYR cc_start: 0.7461 (m-80) cc_final: 0.7229 (m-80) REVERT: C 45 LEU cc_start: 0.9504 (tt) cc_final: 0.9294 (tp) REVERT: D 288 ASN cc_start: 0.9226 (t0) cc_final: 0.8577 (t0) REVERT: E 29 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8092 (t70) REVERT: E 245 GLU cc_start: 0.8183 (tp30) cc_final: 0.7972 (tp30) REVERT: F 29 ASP cc_start: 0.8188 (t70) cc_final: 0.7660 (t0) REVERT: F 115 GLU cc_start: 0.8042 (tt0) cc_final: 0.7699 (tt0) REVERT: F 337 MET cc_start: 0.8636 (mtt) cc_final: 0.7845 (tmm) outliers start: 32 outliers final: 19 residues processed: 225 average time/residue: 0.0996 time to fit residues: 35.8319 Evaluate side-chains 198 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 89 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 182 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS ** B 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** F 312 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093113 restraints weight = 37027.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095858 restraints weight = 17044.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097552 restraints weight = 10528.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098627 restraints weight = 7953.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099120 restraints weight = 6793.853| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1768 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= 0.117 Angle : 0.528 10.808 22258 Z= 0.280 Chirality : 0.040 0.194 2408 Planarity : 0.003 0.039 2673 Dihedral : 7.342 58.753 2298 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.06 % Allowed : 13.52 % Favored : 84.42 % 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 aren not related in a simple way. whole: 0.90 (0.20), residues: 1842 helix: 1.35 (0.15), residues: 1284 sheet: 0.46 (0.52), residues: 96 loop : -1.49 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 309 TYR 0.022 0.001 TYR E 325 PHE 0.014 0.001 PHE B 144 TRP 0.019 0.001 TRP B 143 HIS 0.011 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00256 (16473) covalent geometry : angle 0.52755 (22222) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.56655 ( 36) hydrogen bonds : bond 0.03933 ( 996) hydrogen bonds : angle 3.61891 ( 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 234 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9202 (tp) cc_final: 0.8957 (tt) REVERT: A 162 LYS cc_start: 0.8544 (mmpt) cc_final: 0.7991 (mtmm) REVERT: A 343 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8011 (ttt) REVERT: A 357 ARG cc_start: 0.7102 (ptp-170) cc_final: 0.6757 (ptp-170) REVERT: B 292 ASP cc_start: 0.8409 (m-30) cc_final: 0.8020 (p0) REVERT: C 17 TYR cc_start: 0.7387 (m-80) cc_final: 0.7153 (m-80) REVERT: C 29 ASP cc_start: 0.8760 (t0) cc_final: 0.8498 (t0) REVERT: C 45 LEU cc_start: 0.9526 (tt) cc_final: 0.9274 (tp) REVERT: C 280 CYS cc_start: 0.8967 (m) cc_final: 0.8530 (m) REVERT: D 328 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7665 (tt) REVERT: D 352 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8774 (t) REVERT: F 115 GLU cc_start: 0.7979 (tt0) cc_final: 0.7704 (tt0) REVERT: F 337 MET cc_start: 0.8673 (mtt) cc_final: 0.7840 (tmm) outliers start: 36 outliers final: 25 residues processed: 221 average time/residue: 0.0995 time to fit residues: 35.5042 Evaluate side-chains 204 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 129 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 chunk 156 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3786 r_free = 0.3786 target = 0.125595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095025 restraints weight = 36920.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097590 restraints weight = 17882.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100171 restraints weight = 9813.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100136 restraints weight = 7363.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100121 restraints weight = 6706.192| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1922 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= 0.115 Angle : 0.534 13.320 22258 Z= 0.278 Chirality : 0.040 0.146 2408 Planarity : 0.003 0.039 2673 Dihedral : 7.053 59.943 2298 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.52 % Allowed : 15.06 % Favored : 82.42 % 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 aren not related in a simple way. whole: 1.09 (0.21), residues: 1842 helix: 1.50 (0.15), residues: 1284 sheet: 0.55 (0.51), residues: 96 loop : -1.44 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.024 0.001 TYR F 325 PHE 0.017 0.001 PHE A 144 TRP 0.021 0.001 TRP A 143 HIS 0.009 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00252 (16473) covalent geometry : angle 0.53353 (22222) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.58432 ( 36) hydrogen bonds : bond 0.03812 ( 996) hydrogen bonds : angle 3.58057 ( 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 239 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9164 (tp) cc_final: 0.8930 (tt) REVERT: A 162 LYS cc_start: 0.8555 (mmpt) cc_final: 0.8014 (mtmm) REVERT: A 357 ARG cc_start: 0.7100 (ptp-170) cc_final: 0.6756 (ptp-170) REVERT: B 292 ASP cc_start: 0.8435 (m-30) cc_final: 0.8024 (p0) REVERT: C 17 TYR cc_start: 0.7399 (m-80) cc_final: 0.7154 (m-80) REVERT: C 29 ASP cc_start: 0.8673 (t0) cc_final: 0.8229 (t0) REVERT: C 280 CYS cc_start: 0.8985 (m) cc_final: 0.8544 (m) REVERT: D 328 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (tt) REVERT: D 352 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8768 (t) REVERT: F 337 MET cc_start: 0.8673 (mtt) cc_final: 0.7835 (tmm) outliers start: 44 outliers final: 30 residues processed: 225 average time/residue: 0.0966 time to fit residues: 34.9684 Evaluate side-chains 212 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN 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 = 0.3751 r_free = 0.3751 target = 0.124002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092855 restraints weight = 36933.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095375 restraints weight = 18214.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097911 restraints weight = 10095.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097741 restraints weight = 7844.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097690 restraints weight = 7207.687| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16491 Z= 0.157 Angle : 0.571 11.678 22258 Z= 0.300 Chirality : 0.041 0.144 2408 Planarity : 0.003 0.040 2673 Dihedral : 6.974 57.605 2298 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.81 % Allowed : 16.15 % Favored : 81.04 % 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 aren not related in a simple way. whole: 1.08 (0.21), residues: 1842 helix: 1.57 (0.15), residues: 1272 sheet: 0.59 (0.50), residues: 96 loop : -1.64 (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 0.014 0.001 PHE B 372 TRP 0.021 0.001 TRP B 168 HIS 0.010 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00359 (16473) covalent geometry : angle 0.57104 (22222) SS BOND : bond 0.00260 ( 18) SS BOND : angle 0.68002 ( 36) hydrogen bonds : bond 0.04232 ( 996) hydrogen bonds : angle 3.68709 ( 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 237 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9225 (tp) cc_final: 0.9013 (tt) REVERT: A 162 LYS cc_start: 0.8467 (mmpt) cc_final: 0.7885 (mtmm) REVERT: B 292 ASP cc_start: 0.8379 (m-30) cc_final: 0.8010 (p0) REVERT: C 17 TYR cc_start: 0.7428 (m-80) cc_final: 0.7133 (m-80) REVERT: C 29 ASP cc_start: 0.8680 (t0) cc_final: 0.8244 (t0) REVERT: C 280 CYS cc_start: 0.8915 (m) cc_final: 0.8354 (m) REVERT: D 352 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8896 (t) REVERT: E 236 GLU cc_start: 0.8065 (tp30) cc_final: 0.7236 (mp0) REVERT: F 239 GLN cc_start: 0.7341 (mp10) cc_final: 0.7072 (pm20) outliers start: 49 outliers final: 34 residues processed: 219 average time/residue: 0.0925 time to fit residues: 32.6977 Evaluate side-chains 204 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 20 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 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: 4.9990 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 406 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN 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 = 0.3764 r_free = 0.3764 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092715 restraints weight = 36452.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095442 restraints weight = 17115.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097176 restraints weight = 10631.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098249 restraints weight = 8036.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098638 restraints weight = 6859.303| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2076 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= 0.128 Angle : 0.556 10.952 22258 Z= 0.291 Chirality : 0.040 0.161 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.793 58.359 2298 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.98 % Allowed : 17.01 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1842 helix: 1.62 (0.15), residues: 1272 sheet: 0.76 (0.51), residues: 96 loop : -1.56 (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 0.021 0.001 TRP B 168 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00286 (16473) covalent geometry : angle 0.55622 (22222) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.57261 ( 36) hydrogen bonds : bond 0.04009 ( 996) hydrogen bonds : angle 3.63368 ( 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 235 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9233 (tp) cc_final: 0.9008 (tt) REVERT: A 162 LYS cc_start: 0.8542 (mmpt) cc_final: 0.7969 (mtmm) REVERT: A 357 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6691 (ptp-110) REVERT: B 292 ASP cc_start: 0.8390 (m-30) cc_final: 0.8033 (p0) REVERT: C 17 TYR cc_start: 0.7355 (m-80) cc_final: 0.7074 (m-80) REVERT: C 29 ASP cc_start: 0.8655 (t0) cc_final: 0.8231 (t0) REVERT: C 280 CYS cc_start: 0.8875 (m) cc_final: 0.8349 (m) REVERT: D 352 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8898 (t) REVERT: E 35 MET cc_start: 0.8431 (mtp) cc_final: 0.8188 (mtp) REVERT: E 236 GLU cc_start: 0.8042 (tp30) cc_final: 0.7218 (mp0) outliers start: 52 outliers final: 36 residues processed: 222 average time/residue: 0.0943 time to fit residues: 34.1909 Evaluate side-chains 216 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 36 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 151 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 4 optimal weight: 0.0570 chunk 167 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS D 400 ASN E 404 GLN ** 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 = 0.3799 r_free = 0.3799 target = 0.126438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095721 restraints weight = 36856.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098459 restraints weight = 17339.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101006 restraints weight = 9508.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100838 restraints weight = 7293.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100763 restraints weight = 6737.632| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16491 Z= 0.104 Angle : 0.541 11.660 22258 Z= 0.282 Chirality : 0.039 0.166 2408 Planarity : 0.003 0.037 2673 Dihedral : 6.409 59.402 2298 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.81 % Allowed : 17.64 % Favored : 79.55 % 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 aren not related in a simple way. whole: 1.30 (0.21), residues: 1842 helix: 1.72 (0.15), residues: 1272 sheet: 0.94 (0.52), residues: 96 loop : -1.55 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 309 TYR 0.029 0.001 TYR E 325 PHE 0.013 0.001 PHE B 144 TRP 0.025 0.001 TRP B 168 HIS 0.013 0.001 HIS C 155 Details of bonding type rmsd covalent geometry : bond 0.00220 (16473) covalent geometry : angle 0.54133 (22222) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.45629 ( 36) hydrogen bonds : bond 0.03590 ( 996) hydrogen bonds : angle 3.52166 ( 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 252 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9151 (tp) cc_final: 0.8917 (tt) REVERT: A 162 LYS cc_start: 0.8461 (mmpt) cc_final: 0.7908 (mtmm) REVERT: A 357 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6495 (ptp-110) REVERT: B 292 ASP cc_start: 0.8435 (m-30) cc_final: 0.8024 (p0) REVERT: C 17 TYR cc_start: 0.7329 (m-80) cc_final: 0.7052 (m-80) REVERT: C 29 ASP cc_start: 0.8662 (t0) cc_final: 0.8225 (t0) REVERT: C 280 CYS cc_start: 0.8918 (m) cc_final: 0.8497 (m) REVERT: D 352 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8861 (t) REVERT: D 404 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6329 (mp-120) REVERT: E 35 MET cc_start: 0.8404 (mtp) cc_final: 0.8194 (mtp) REVERT: E 236 GLU cc_start: 0.8091 (tp30) cc_final: 0.7309 (mp0) REVERT: F 104 HIS cc_start: 0.8955 (OUTLIER) cc_final: 0.8080 (t70) outliers start: 49 outliers final: 38 residues processed: 239 average time/residue: 0.0959 time to fit residues: 36.9820 Evaluate side-chains 227 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 160 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 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 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 277 LEU 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 343 MET Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** C 155 HIS C 288 ASN D 400 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094295 restraints weight = 37033.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096873 restraints weight = 17142.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099399 restraints weight = 9540.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099316 restraints weight = 7224.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099273 restraints weight = 6613.934| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16491 Z= 0.119 Angle : 0.578 12.292 22258 Z= 0.295 Chirality : 0.040 0.173 2408 Planarity : 0.003 0.037 2673 Dihedral : 6.318 59.626 2298 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.58 % Allowed : 18.10 % 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 aren not related in a simple way. whole: 1.32 (0.21), residues: 1842 helix: 1.71 (0.15), residues: 1272 sheet: 0.99 (0.52), residues: 96 loop : -1.50 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 251 TYR 0.030 0.001 TYR F 325 PHE 0.033 0.001 PHE B 156 TRP 0.024 0.001 TRP B 168 HIS 0.013 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00265 (16473) covalent geometry : angle 0.57785 (22222) SS BOND : bond 0.00196 ( 18) SS BOND : angle 0.67311 ( 36) hydrogen bonds : bond 0.03698 ( 996) hydrogen bonds : angle 3.55869 ( 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 231 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8463 (mmpt) cc_final: 0.7912 (mtmm) REVERT: A 357 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6513 (ptp-110) REVERT: B 110 ASP cc_start: 0.8065 (m-30) cc_final: 0.7716 (m-30) REVERT: B 292 ASP cc_start: 0.8474 (m-30) cc_final: 0.7974 (p0) REVERT: C 17 TYR cc_start: 0.7351 (m-80) cc_final: 0.7023 (m-80) REVERT: C 29 ASP cc_start: 0.8659 (t0) cc_final: 0.8321 (t0) REVERT: C 280 CYS cc_start: 0.8912 (m) cc_final: 0.8492 (m) REVERT: D 352 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8862 (t) REVERT: D 404 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6329 (mp-120) REVERT: E 35 MET cc_start: 0.8446 (mtp) cc_final: 0.8178 (mtp) REVERT: E 236 GLU cc_start: 0.7979 (tp30) cc_final: 0.7219 (mp0) REVERT: E 245 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7686 (tp30) REVERT: F 104 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8170 (t70) outliers start: 45 outliers final: 36 residues processed: 219 average time/residue: 0.0912 time to fit residues: 32.4601 Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 TRP 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 D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 277 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 37 MET 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 Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 253 HIS B 116 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3738 r_free = 0.3738 target = 0.122433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091728 restraints weight = 37140.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094268 restraints weight = 17490.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097057 restraints weight = 9579.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096495 restraints weight = 7102.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096502 restraints weight = 7057.564| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16491 Z= 0.182 Angle : 0.627 12.882 22258 Z= 0.324 Chirality : 0.042 0.199 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.461 57.512 2298 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.52 % Allowed : 18.27 % Favored : 79.21 % 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 aren not related in a simple way. whole: 1.19 (0.21), residues: 1842 helix: 1.61 (0.15), residues: 1272 sheet: 0.95 (0.51), residues: 96 loop : -1.53 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.035 0.001 TYR F 325 PHE 0.023 0.001 PHE B 372 TRP 0.025 0.001 TRP B 168 HIS 0.013 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00420 (16473) covalent geometry : angle 0.62649 (22222) SS BOND : bond 0.00367 ( 18) SS BOND : angle 0.84419 ( 36) hydrogen bonds : bond 0.04203 ( 996) hydrogen bonds : angle 3.75248 ( 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 223 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8516 (mmpt) cc_final: 0.7949 (mtmm) REVERT: A 357 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6353 (ptp-110) REVERT: C 29 ASP cc_start: 0.8691 (t0) cc_final: 0.8369 (t0) REVERT: C 280 CYS cc_start: 0.8910 (m) cc_final: 0.8331 (m) REVERT: D 352 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8870 (t) REVERT: E 236 GLU cc_start: 0.8027 (tp30) cc_final: 0.7226 (mp0) REVERT: E 245 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7705 (tp30) REVERT: F 104 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8352 (t70) outliers start: 44 outliers final: 36 residues processed: 210 average time/residue: 0.0849 time to fit residues: 29.1422 Evaluate side-chains 215 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 TRP Chi-restraints excluded: chain B residue 279 ILE 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 D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 277 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 265 MET 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 95 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 253 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN C 288 ASN D 400 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.123146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091557 restraints weight = 36865.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094253 restraints weight = 17361.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095945 restraints weight = 10857.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096989 restraints weight = 8246.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097515 restraints weight = 7069.944| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2352 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= 0.131 Angle : 0.598 13.069 22258 Z= 0.308 Chirality : 0.041 0.186 2408 Planarity : 0.003 0.037 2673 Dihedral : 6.310 53.139 2298 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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 aren not related in a simple way. whole: 1.30 (0.21), residues: 1842 helix: 1.68 (0.15), residues: 1266 sheet: 0.98 (0.51), residues: 96 loop : -1.38 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 251 TYR 0.030 0.001 TYR E 325 PHE 0.022 0.001 PHE B 372 TRP 0.025 0.001 TRP B 168 HIS 0.008 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00295 (16473) covalent geometry : angle 0.59823 (22222) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.63371 ( 36) hydrogen bonds : bond 0.03955 ( 996) hydrogen bonds : angle 3.68151 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.44 seconds wall clock time: 39 minutes 16.93 seconds (2356.93 seconds total)