Starting phenix.real_space_refine on Sat Jun 14 19:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.map" model { file = "/net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m19_23616/06_2025/7m19_23616.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10639 2.51 5 N 2532 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.99, per 1000 atoms: 0.69 Number of scatterers: 16039 At special positions: 0 Unit cell: (110.289, 101.193, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.04 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 11 sheets defined 74.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.668A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 23 through 49 removed outlier: 3.509A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 120 through 146 Proline residue: A 126 - end of helix removed outlier: 4.406A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.403A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.013A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.642A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.611A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.618A pdb=" N LEU A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.820A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 Processing helix chain 'B' and resid 26 through 49 removed outlier: 3.811A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.540A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 146 removed outlier: 3.739A pdb=" N PHE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.805A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.462A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 4.097A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 258 through 286 removed outlier: 3.959A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 347 removed outlier: 4.021A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.906A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.495A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.687A pdb=" N PHE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.620A pdb=" N PHE C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.888A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 4.770A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.382A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.999A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.514A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.998A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 4.012A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.898A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.168A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 22 removed outlier: 4.113A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Proline residue: D 22 - end of helix Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.631A pdb=" N PHE D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.739A pdb=" N ARG D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 146 removed outlier: 3.544A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.093A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.324A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.008A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 255 removed outlier: 3.501A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.802A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.966A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.649A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.583A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Proline residue: E 22 - end of helix Processing helix chain 'E' and resid 23 through 49 removed outlier: 3.534A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.510A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 146 removed outlier: 3.644A pdb=" N PHE E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.561A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.449A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.747A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 3.726A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.167A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.601A pdb=" N PHE F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 removed outlier: 3.581A pdb=" N ARG F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 146 removed outlier: 3.638A pdb=" N PHE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.628A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.071A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 4.120A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 Processing helix chain 'F' and resid 258 through 286 removed outlier: 3.844A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.535A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.367A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.891A pdb=" N VAL D 293 " --> pdb=" O CYS D 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.555A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.814A pdb=" N VAL F 293 " --> pdb=" O CYS F 310 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2379 1.31 - 1.44: 4937 1.44 - 1.57: 9006 1.57 - 1.69: 5 1.69 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C18 PEE C 903 " pdb=" C19 PEE C 903 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE F 902 " pdb=" C19 PEE F 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE C 904 " pdb=" C19 PEE C 904 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE E 902 " pdb=" C19 PEE E 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 21581 2.46 - 4.91: 491 4.91 - 7.37: 75 7.37 - 9.82: 37 9.82 - 12.28: 38 Bond angle restraints: 22222 Sorted by residual: angle pdb=" C THR E 48 " pdb=" N GLN E 49 " pdb=" CA GLN E 49 " ideal model delta sigma weight residual 121.90 114.34 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" N GLU E 154 " pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " ideal model delta sigma weight residual 110.28 118.21 -7.93 1.55e+00 4.16e-01 2.62e+01 angle pdb=" C ASN F 370 " pdb=" N ASP F 371 " pdb=" CA ASP F 371 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLU F 245 " pdb=" N LYS F 246 " pdb=" CA LYS F 246 " ideal model delta sigma weight residual 120.68 113.66 7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C CYS B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta sigma weight residual 122.36 115.31 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 9067 24.81 - 49.61: 640 49.61 - 74.42: 45 74.42 - 99.23: 14 99.23 - 124.03: 8 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER D 352 " pdb=" C SER D 352 " pdb=" N PHE D 353 " pdb=" CA PHE D 353 " ideal model delta harmonic sigma weight residual 180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C12 PEE B 902 " pdb=" C10 PEE B 902 " pdb=" C11 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sinusoidal sigma weight residual -19.47 104.56 -124.03 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1922 0.062 - 0.124: 434 0.124 - 0.186: 48 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CB VAL E 297 " pdb=" CA VAL E 297 " pdb=" CG1 VAL E 297 " pdb=" CG2 VAL E 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C05 YNJ C 902 " pdb=" C06 YNJ C 902 " pdb=" C13 YNJ C 902 " pdb=" C27 YNJ C 902 " both_signs ideal model delta sigma weight residual False 3.00 2.70 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 275 " -0.018 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 275 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 275 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 275 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 275 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 244 " -0.018 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE E 244 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 244 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 244 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 244 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 244 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 136 " -0.020 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE C 136 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 136 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 136 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 136 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2744 2.77 - 3.30: 15064 3.30 - 3.83: 26554 3.83 - 4.37: 28621 4.37 - 4.90: 50238 Nonbonded interactions: 123221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.231 3.040 nonbonded pdb=" O THR D 44 " pdb=" OG1 THR D 48 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP E 50 " pdb=" OH TYR E 114 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP C 50 " pdb=" OH TYR C 114 " model vdw 2.273 3.040 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.273 3.040 ... (remaining 123216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 408 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or resid 903)) selection = (chain 'B' and (resid 15 through 408 or resid 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 C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or resid 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 C1 \ 7 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 408 or resid 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 C1 \ 7 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 408 or resid 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 C1 \ 7 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 408 or resid 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 C1 \ 7 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.350 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.150 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.183 16491 Z= 0.470 Angle : 1.030 12.279 22258 Z= 0.508 Chirality : 0.052 0.310 2408 Planarity : 0.005 0.042 2673 Dihedral : 15.738 124.033 6060 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1842 helix: 0.04 (0.14), residues: 1236 sheet: 0.66 (0.49), residues: 96 loop : -1.95 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 143 HIS 0.019 0.002 HIS E 377 PHE 0.057 0.002 PHE D 275 TYR 0.022 0.002 TYR A 332 ARG 0.007 0.000 ARG D 357 Details of bonding type rmsd hydrogen bonds : bond 0.11051 ( 1005) hydrogen bonds : angle 5.31539 ( 2949) SS BOND : bond 0.00286 ( 18) SS BOND : angle 0.71087 ( 36) covalent geometry : bond 0.00946 (16473) covalent geometry : angle 1.03056 (22222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8215 (tmt-80) cc_final: 0.7964 (tpt170) REVERT: B 325 TYR cc_start: 0.8747 (t80) cc_final: 0.8428 (t80) REVERT: C 336 CYS cc_start: 0.8318 (m) cc_final: 0.8114 (t) REVERT: D 37 MET cc_start: 0.8513 (ptp) cc_final: 0.8311 (ptt) REVERT: D 351 TYR cc_start: 0.6384 (t80) cc_final: 0.5922 (t80) REVERT: D 399 GLU cc_start: 0.8353 (mp0) cc_final: 0.7554 (mp0) REVERT: E 162 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8758 (mmtm) REVERT: F 249 LYS cc_start: 0.9154 (tptt) cc_final: 0.8574 (pttt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2684 time to fit residues: 104.9135 Evaluate side-chains 187 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 155 HIS A 288 ASN B 253 HIS B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098427 restraints weight = 36642.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101101 restraints weight = 15481.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102866 restraints weight = 8375.813| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16491 Z= 0.178 Angle : 0.594 11.220 22258 Z= 0.322 Chirality : 0.042 0.139 2408 Planarity : 0.003 0.032 2673 Dihedral : 9.573 83.050 2298 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.83 % Allowed : 10.02 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1842 helix: 0.88 (0.15), residues: 1284 sheet: 0.92 (0.49), residues: 96 loop : -1.86 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 143 HIS 0.007 0.001 HIS B 253 PHE 0.020 0.002 PHE C 136 TYR 0.017 0.001 TYR D 332 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1005) hydrogen bonds : angle 4.05276 ( 2949) SS BOND : bond 0.00330 ( 18) SS BOND : angle 0.73942 ( 36) covalent geometry : bond 0.00402 (16473) covalent geometry : angle 0.59327 (22222) *********************** 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 222 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8148 (tmt-80) cc_final: 0.7885 (tpt170) REVERT: A 288 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9130 (t0) REVERT: B 17 TYR cc_start: 0.7550 (m-10) cc_final: 0.7326 (m-10) REVERT: B 325 TYR cc_start: 0.8870 (t80) cc_final: 0.8579 (t80) REVERT: C 161 LEU cc_start: 0.8804 (mm) cc_final: 0.8498 (mm) REVERT: E 162 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8513 (mmtm) REVERT: E 168 TRP cc_start: 0.7259 (t60) cc_final: 0.6701 (t60) REVERT: F 154 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8442 (mm-30) REVERT: F 249 LYS cc_start: 0.9184 (tptt) cc_final: 0.8596 (pttt) REVERT: F 289 ILE cc_start: 0.8985 (pt) cc_final: 0.8732 (mt) outliers start: 32 outliers final: 17 residues processed: 207 average time/residue: 0.2917 time to fit residues: 95.3737 Evaluate side-chains 189 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.0970 chunk 170 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 166 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 287 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.128632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104538 restraints weight = 36195.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103536 restraints weight = 14218.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104520 restraints weight = 12102.610| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16491 Z= 0.121 Angle : 0.530 9.649 22258 Z= 0.286 Chirality : 0.040 0.120 2408 Planarity : 0.003 0.038 2673 Dihedral : 7.815 69.242 2298 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.72 % Allowed : 14.03 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1842 helix: 1.47 (0.15), residues: 1254 sheet: 1.38 (0.51), residues: 96 loop : -1.39 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 143 HIS 0.009 0.001 HIS B 253 PHE 0.019 0.001 PHE C 136 TYR 0.012 0.001 TYR C 332 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1005) hydrogen bonds : angle 3.76635 ( 2949) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.58716 ( 36) covalent geometry : bond 0.00261 (16473) covalent geometry : angle 0.52955 (22222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8164 (tmt-80) cc_final: 0.7869 (tpt170) REVERT: B 288 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 325 TYR cc_start: 0.8828 (t80) cc_final: 0.8547 (t80) REVERT: B 375 MET cc_start: 0.8743 (mtp) cc_final: 0.8531 (mtp) REVERT: C 161 LEU cc_start: 0.8830 (mm) cc_final: 0.8533 (mm) REVERT: D 161 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7551 (pp) REVERT: D 280 CYS cc_start: 0.8757 (m) cc_final: 0.8409 (m) REVERT: D 399 GLU cc_start: 0.8582 (mp0) cc_final: 0.7837 (mp0) REVERT: E 18 ARG cc_start: 0.7986 (ptp-170) cc_final: 0.7419 (ptp90) REVERT: E 162 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8608 (mmtm) REVERT: F 154 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8373 (mm-30) REVERT: F 245 GLU cc_start: 0.8757 (mp0) cc_final: 0.8350 (mp0) REVERT: F 249 LYS cc_start: 0.9195 (tptt) cc_final: 0.8643 (pttt) outliers start: 30 outliers final: 18 residues processed: 215 average time/residue: 0.2997 time to fit residues: 97.8923 Evaluate side-chains 196 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS E 155 HIS F 288 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.127480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100159 restraints weight = 36014.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102844 restraints weight = 14790.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104285 restraints weight = 8212.099| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1757 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= 0.145 Angle : 0.541 7.939 22258 Z= 0.292 Chirality : 0.041 0.220 2408 Planarity : 0.003 0.028 2673 Dihedral : 7.385 65.487 2298 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.69 % Allowed : 15.52 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1842 helix: 1.63 (0.15), residues: 1260 sheet: 1.56 (0.51), residues: 96 loop : -1.34 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 143 HIS 0.010 0.001 HIS B 253 PHE 0.026 0.001 PHE C 250 TYR 0.018 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1005) hydrogen bonds : angle 3.74565 ( 2949) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.62209 ( 36) covalent geometry : bond 0.00324 (16473) covalent geometry : angle 0.54111 (22222) *********************** 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 233 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8166 (tmt-80) cc_final: 0.7863 (tpt170) REVERT: A 399 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: B 288 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8723 (t0) REVERT: B 325 TYR cc_start: 0.8864 (t80) cc_final: 0.8614 (t80) REVERT: C 161 LEU cc_start: 0.8828 (mm) cc_final: 0.8530 (mm) REVERT: D 351 TYR cc_start: 0.6563 (t80) cc_final: 0.6152 (t80) REVERT: D 399 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 18 ARG cc_start: 0.8031 (ptp-170) cc_final: 0.7440 (ptp90) REVERT: E 162 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8596 (mmtm) REVERT: E 379 ILE cc_start: 0.8334 (tp) cc_final: 0.8118 (tp) REVERT: F 154 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8340 (mm-30) REVERT: F 249 LYS cc_start: 0.9196 (tptt) cc_final: 0.8664 (pttt) REVERT: F 381 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8066 (mm-40) outliers start: 47 outliers final: 29 residues processed: 216 average time/residue: 0.3328 time to fit residues: 109.6907 Evaluate side-chains 207 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 93 optimal weight: 0.0000 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS E 105 GLN E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105597 restraints weight = 36352.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105746 restraints weight = 13963.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106850 restraints weight = 9624.042| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16491 Z= 0.104 Angle : 0.515 10.179 22258 Z= 0.276 Chirality : 0.039 0.181 2408 Planarity : 0.003 0.030 2673 Dihedral : 6.900 63.350 2298 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 17.01 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1842 helix: 1.78 (0.15), residues: 1260 sheet: 1.68 (0.52), residues: 96 loop : -1.31 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 143 HIS 0.019 0.001 HIS B 253 PHE 0.034 0.001 PHE F 244 TYR 0.014 0.001 TYR C 351 ARG 0.001 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1005) hydrogen bonds : angle 3.62768 ( 2949) SS BOND : bond 0.00214 ( 18) SS BOND : angle 0.55797 ( 36) covalent geometry : bond 0.00211 (16473) covalent geometry : angle 0.51473 (22222) *********************** 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 246 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 2.718 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8099 (tmt-80) cc_final: 0.7804 (tpt170) REVERT: A 399 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: B 269 ILE cc_start: 0.8763 (tt) cc_final: 0.8545 (tp) REVERT: B 288 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8683 (t0) REVERT: B 325 TYR cc_start: 0.8807 (t80) cc_final: 0.8485 (t80) REVERT: C 161 LEU cc_start: 0.8826 (mm) cc_final: 0.8550 (mm) REVERT: D 280 CYS cc_start: 0.8778 (m) cc_final: 0.8570 (m) REVERT: D 351 TYR cc_start: 0.6332 (t80) cc_final: 0.6020 (t80) REVERT: E 133 THR cc_start: 0.9495 (m) cc_final: 0.9219 (t) REVERT: E 162 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8592 (mmtm) REVERT: E 379 ILE cc_start: 0.8359 (tp) cc_final: 0.8126 (tp) REVERT: F 249 LYS cc_start: 0.9187 (tptt) cc_final: 0.8642 (pttt) REVERT: F 380 ASP cc_start: 0.8056 (t70) cc_final: 0.7530 (t0) REVERT: F 381 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8155 (mm-40) outliers start: 40 outliers final: 23 residues processed: 234 average time/residue: 0.3005 time to fit residues: 107.9858 Evaluate side-chains 215 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 375 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 67 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102900 restraints weight = 36240.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104269 restraints weight = 14894.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104944 restraints weight = 9669.340| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2021 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= 0.123 Angle : 0.525 9.088 22258 Z= 0.281 Chirality : 0.040 0.193 2408 Planarity : 0.003 0.028 2673 Dihedral : 6.689 61.529 2298 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.35 % Allowed : 17.70 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1842 helix: 1.84 (0.15), residues: 1260 sheet: 1.72 (0.51), residues: 96 loop : -1.32 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 342 HIS 0.010 0.001 HIS B 253 PHE 0.025 0.001 PHE F 244 TYR 0.015 0.001 TYR E 332 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1005) hydrogen bonds : angle 3.63364 ( 2949) SS BOND : bond 0.00229 ( 18) SS BOND : angle 0.58293 ( 36) covalent geometry : bond 0.00271 (16473) covalent geometry : angle 0.52460 (22222) *********************** 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 231 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8119 (tmt-80) cc_final: 0.7806 (tpt170) REVERT: A 399 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: B 269 ILE cc_start: 0.8770 (tt) cc_final: 0.8565 (tp) REVERT: B 288 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8719 (t0) REVERT: B 325 TYR cc_start: 0.8834 (t80) cc_final: 0.8565 (t80) REVERT: C 161 LEU cc_start: 0.8836 (mm) cc_final: 0.8556 (mm) REVERT: D 280 CYS cc_start: 0.8783 (m) cc_final: 0.8561 (m) REVERT: D 351 TYR cc_start: 0.6309 (t80) cc_final: 0.6033 (t80) REVERT: E 18 ARG cc_start: 0.7807 (ptp-170) cc_final: 0.7362 (ptp90) REVERT: E 162 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8596 (mmtm) REVERT: F 249 LYS cc_start: 0.9186 (tptt) cc_final: 0.8630 (pttt) REVERT: F 380 ASP cc_start: 0.8064 (t70) cc_final: 0.7564 (t0) REVERT: F 381 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8222 (mm-40) outliers start: 41 outliers final: 32 residues processed: 218 average time/residue: 0.2549 time to fit residues: 85.1634 Evaluate side-chains 206 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 173 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS E 105 GLN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099418 restraints weight = 36476.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101793 restraints weight = 15649.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103406 restraints weight = 8674.037| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16491 Z= 0.174 Angle : 0.570 8.447 22258 Z= 0.305 Chirality : 0.042 0.211 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.840 60.533 2298 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.21 % Allowed : 18.44 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1842 helix: 1.70 (0.15), residues: 1284 sheet: 1.78 (0.50), residues: 96 loop : -1.54 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 143 HIS 0.018 0.001 HIS B 253 PHE 0.015 0.001 PHE F 125 TYR 0.016 0.001 TYR C 351 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 1005) hydrogen bonds : angle 3.76315 ( 2949) SS BOND : bond 0.00308 ( 18) SS BOND : angle 0.70261 ( 36) covalent geometry : bond 0.00397 (16473) covalent geometry : angle 0.56995 (22222) *********************** 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 238 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8240 (tmt-80) cc_final: 0.7923 (tpt170) REVERT: A 399 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: B 269 ILE cc_start: 0.8779 (tt) cc_final: 0.8576 (tp) REVERT: B 288 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8829 (t0) REVERT: B 325 TYR cc_start: 0.8887 (t80) cc_final: 0.8644 (t80) REVERT: C 161 LEU cc_start: 0.8859 (mm) cc_final: 0.8570 (mm) REVERT: C 275 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8644 (t80) REVERT: D 280 CYS cc_start: 0.8750 (m) cc_final: 0.8501 (m) REVERT: D 351 TYR cc_start: 0.6562 (t80) cc_final: 0.6172 (t80) REVERT: E 18 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.7343 (ptp90) REVERT: F 249 LYS cc_start: 0.9194 (tptt) cc_final: 0.8616 (pttt) REVERT: F 381 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8136 (mm-40) outliers start: 56 outliers final: 44 residues processed: 219 average time/residue: 0.2591 time to fit residues: 86.7061 Evaluate side-chains 216 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain 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 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 144 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 105 GLN E 116 ASN E 155 HIS ** E 267 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102164 restraints weight = 36150.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104339 restraints weight = 17100.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106931 restraints weight = 9003.514| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16491 Z= 0.109 Angle : 0.531 9.859 22258 Z= 0.282 Chirality : 0.040 0.211 2408 Planarity : 0.003 0.029 2673 Dihedral : 6.402 59.395 2298 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.63 % Allowed : 19.01 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.21), residues: 1842 helix: 1.87 (0.15), residues: 1260 sheet: 1.83 (0.51), residues: 96 loop : -1.28 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 143 HIS 0.011 0.001 HIS B 253 PHE 0.013 0.001 PHE B 125 TYR 0.013 0.001 TYR C 351 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1005) hydrogen bonds : angle 3.60765 ( 2949) SS BOND : bond 0.00205 ( 18) SS BOND : angle 0.50562 ( 36) covalent geometry : bond 0.00230 (16473) covalent geometry : angle 0.53083 (22222) *********************** 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 242 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8253 (tmt-80) cc_final: 0.7895 (tpt170) REVERT: A 399 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7283 (pt0) REVERT: B 143 TRP cc_start: 0.8446 (t60) cc_final: 0.8139 (t60) REVERT: B 269 ILE cc_start: 0.8740 (tt) cc_final: 0.8540 (tp) REVERT: B 288 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8699 (t0) REVERT: B 325 TYR cc_start: 0.8800 (t80) cc_final: 0.8492 (t80) REVERT: C 161 LEU cc_start: 0.8853 (mm) cc_final: 0.8571 (mm) REVERT: C 275 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8592 (t80) REVERT: D 280 CYS cc_start: 0.8680 (m) cc_final: 0.8375 (m) REVERT: D 351 TYR cc_start: 0.6316 (t80) cc_final: 0.5994 (t80) REVERT: E 18 ARG cc_start: 0.7868 (ptp-170) cc_final: 0.7338 (ptp90) REVERT: E 162 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8562 (mmtm) REVERT: F 249 LYS cc_start: 0.9169 (tptt) cc_final: 0.8574 (pttt) outliers start: 46 outliers final: 38 residues processed: 224 average time/residue: 0.2498 time to fit residues: 86.6967 Evaluate side-chains 217 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 152 optimal weight: 0.0870 chunk 128 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS D 400 ASN E 155 HIS ** E 267 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.129842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103126 restraints weight = 35848.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105232 restraints weight = 17282.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107515 restraints weight = 9114.789| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16491 Z= 0.114 Angle : 0.543 9.444 22258 Z= 0.286 Chirality : 0.041 0.271 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.236 58.625 2298 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.81 % Allowed : 19.36 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1842 helix: 1.91 (0.15), residues: 1260 sheet: 1.94 (0.51), residues: 96 loop : -1.29 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.014 0.001 HIS B 253 PHE 0.016 0.001 PHE A 250 TYR 0.030 0.001 TYR D 325 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1005) hydrogen bonds : angle 3.60441 ( 2949) SS BOND : bond 0.00205 ( 18) SS BOND : angle 0.52940 ( 36) covalent geometry : bond 0.00247 (16473) covalent geometry : angle 0.54330 (22222) *********************** 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 237 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8263 (tmt-80) cc_final: 0.7902 (tpt170) REVERT: A 288 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8424 (t0) REVERT: A 399 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: B 143 TRP cc_start: 0.8452 (t60) cc_final: 0.8147 (t60) REVERT: B 269 ILE cc_start: 0.8745 (tt) cc_final: 0.8544 (tp) REVERT: B 288 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8717 (t0) REVERT: B 325 TYR cc_start: 0.8806 (t80) cc_final: 0.8501 (t80) REVERT: C 161 LEU cc_start: 0.8851 (mm) cc_final: 0.8570 (mm) REVERT: C 275 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8535 (t80) REVERT: D 280 CYS cc_start: 0.8635 (m) cc_final: 0.8344 (m) REVERT: D 351 TYR cc_start: 0.6334 (t80) cc_final: 0.6000 (t80) REVERT: E 18 ARG cc_start: 0.7866 (ptp-170) cc_final: 0.7341 (ptp90) REVERT: E 162 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8574 (mmtm) REVERT: F 249 LYS cc_start: 0.9199 (tptt) cc_final: 0.8583 (pttt) outliers start: 49 outliers final: 41 residues processed: 222 average time/residue: 0.2501 time to fit residues: 85.6910 Evaluate side-chains 223 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 46 optimal weight: 0.0370 chunk 70 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 91 optimal weight: 0.0000 chunk 21 optimal weight: 0.0970 overall best weight: 0.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 155 HIS E 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.131129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105964 restraints weight = 36019.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107253 restraints weight = 15143.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107646 restraints weight = 10162.686| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16491 Z= 0.108 Angle : 0.538 10.430 22258 Z= 0.283 Chirality : 0.040 0.258 2408 Planarity : 0.003 0.028 2673 Dihedral : 6.058 59.873 2298 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.52 % Allowed : 19.87 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1842 helix: 1.91 (0.15), residues: 1260 sheet: 2.03 (0.52), residues: 96 loop : -1.27 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 143 HIS 0.012 0.001 HIS B 253 PHE 0.016 0.001 PHE A 250 TYR 0.027 0.001 TYR D 325 ARG 0.001 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 1005) hydrogen bonds : angle 3.57076 ( 2949) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.48157 ( 36) covalent geometry : bond 0.00227 (16473) covalent geometry : angle 0.53810 (22222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8237 (tmt-80) cc_final: 0.7902 (tpt170) REVERT: A 173 LEU cc_start: 0.8623 (mm) cc_final: 0.8364 (mm) REVERT: A 288 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 399 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: B 143 TRP cc_start: 0.8414 (t60) cc_final: 0.8108 (t60) REVERT: B 288 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8703 (t0) REVERT: B 325 TYR cc_start: 0.8776 (t80) cc_final: 0.8448 (t80) REVERT: C 161 LEU cc_start: 0.8845 (mm) cc_final: 0.8573 (mm) REVERT: C 275 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8546 (t80) REVERT: D 280 CYS cc_start: 0.8603 (m) cc_final: 0.8358 (m) REVERT: D 351 TYR cc_start: 0.6207 (t80) cc_final: 0.5983 (t80) REVERT: E 18 ARG cc_start: 0.7844 (ptp-170) cc_final: 0.7343 (ptp90) REVERT: E 162 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8605 (mmtm) REVERT: F 249 LYS cc_start: 0.9191 (tptt) cc_final: 0.8590 (pttt) outliers start: 44 outliers final: 36 residues processed: 230 average time/residue: 0.2568 time to fit residues: 91.4856 Evaluate side-chains 225 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 175 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104688 restraints weight = 35692.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106170 restraints weight = 13429.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107468 restraints weight = 8640.247| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16491 Z= 0.115 Angle : 0.548 12.738 22258 Z= 0.287 Chirality : 0.041 0.290 2408 Planarity : 0.003 0.028 2673 Dihedral : 5.946 56.274 2298 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.86 % Allowed : 19.70 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1842 helix: 1.91 (0.15), residues: 1260 sheet: 2.11 (0.52), residues: 96 loop : -1.26 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 342 HIS 0.012 0.001 HIS B 253 PHE 0.015 0.001 PHE A 250 TYR 0.027 0.001 TYR D 325 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1005) hydrogen bonds : angle 3.58631 ( 2949) SS BOND : bond 0.00202 ( 18) SS BOND : angle 0.50592 ( 36) covalent geometry : bond 0.00253 (16473) covalent geometry : angle 0.54788 (22222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.47 seconds wall clock time: 100 minutes 27.44 seconds (6027.44 seconds total)