Starting phenix.real_space_refine on Sun Sep 13 02:07:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbm_21593/09_2026/6wbm_21593.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 12943 2.51 5 N 2863 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19201 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 179 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 3.70, per 1000 atoms: 0.19 Number of scatterers: 19201 At special positions: 0 Unit cell: (108.808, 108.808, 120.988, 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) S 77 16.00 P 21 15.00 O 3297 8.00 N 2863 7.00 C 12943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 715.5 milliseconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 71.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.691A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.542A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.691A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 131 removed outlier: 4.083A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 304 through 311 removed outlier: 4.182A pdb=" N VAL B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.690A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 removed outlier: 3.585A pdb=" N PHE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 311 removed outlier: 4.180A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.691A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 removed outlier: 3.585A pdb=" N PHE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 311 removed outlier: 4.180A pdb=" N VAL D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.690A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.081A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.702A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.691A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.566A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.691A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 131 removed outlier: 4.081A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 358 removed outlier: 3.542A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.566A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 1212 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2859 1.32 - 1.44: 4862 1.44 - 1.57: 11767 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 19621 Sorted by residual: bond pdb=" N VAL C 342 " pdb=" CA VAL C 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.98e+00 bond pdb=" N VAL D 342 " pdb=" CA VAL D 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL E 342 " pdb=" CA VAL E 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.95e+00 ... (remaining 19616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25827 2.02 - 4.03: 675 4.03 - 6.05: 91 6.05 - 8.06: 21 8.06 - 10.08: 14 Bond angle restraints: 26628 Sorted by residual: angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 112.12 109.05 3.07 8.40e-01 1.42e+00 1.33e+01 angle pdb=" N ILE E 58 " pdb=" CA ILE E 58 " pdb=" C ILE E 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.30e+01 angle pdb=" N ILE G 58 " pdb=" CA ILE G 58 " pdb=" C ILE G 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE D 58 " pdb=" CA ILE D 58 " pdb=" C ILE D 58 " ideal model delta sigma weight residual 112.12 109.11 3.01 8.40e-01 1.42e+00 1.28e+01 ... (remaining 26623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 11102 31.50 - 63.00: 483 63.00 - 94.50: 14 94.50 - 125.99: 0 125.99 - 157.49: 21 Dihedral angle restraints: 11620 sinusoidal: 4515 harmonic: 7105 Sorted by residual: dihedral pdb=" N1 PTY B 402 " pdb=" C2 PTY B 402 " pdb=" C3 PTY B 402 " pdb=" O11 PTY B 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY E 402 " pdb=" C2 PTY E 402 " pdb=" C3 PTY E 402 " pdb=" O11 PTY E 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY F 402 " pdb=" C2 PTY F 402 " pdb=" C3 PTY F 402 " pdb=" O11 PTY F 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.20 -157.47 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 11617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1991 0.034 - 0.067: 786 0.067 - 0.101: 255 0.101 - 0.135: 89 0.135 - 0.168: 36 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CA LEU F 200 " pdb=" N LEU F 200 " pdb=" C LEU F 200 " pdb=" CB LEU F 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU A 200 " pdb=" N LEU A 200 " pdb=" C LEU A 200 " pdb=" CB LEU A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA LEU E 200 " pdb=" N LEU E 200 " pdb=" C LEU E 200 " pdb=" CB LEU E 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 3154 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 93 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C SER B 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER B 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER C 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER C 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER A 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER A 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1513 2.73 - 3.27: 20315 3.27 - 3.82: 31173 3.82 - 4.36: 36916 4.36 - 4.90: 63155 Nonbonded interactions: 153072 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.237 3.040 ... (remaining 153067 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 2 through 403 or resid 405)) selection = (chain 'B' and (resid 2 through 403 or resid 405)) selection = (chain 'C' and (resid 2 through 403 or resid 405)) selection = (chain 'D' and (resid 2 through 403 or resid 405)) selection = (chain 'E' and (resid 2 through 403 or resid 405)) selection = (chain 'F' and (resid 2 through 403 or resid 405)) selection = (chain 'G' and (resid 2 through 403 or resid 405)) } 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 individual isotropic 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.880 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.007 0.050 19635 Z= 0.366 Angle : 0.803 10.076 26656 Z= 0.454 Chirality : 0.045 0.168 3157 Planarity : 0.004 0.026 3115 Dihedral : 17.566 157.493 6958 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.80 % Allowed : 13.15 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2359 helix: -0.23 (0.12), residues: 1568 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 254 TYR 0.011 0.001 TYR B 345 PHE 0.008 0.001 PHE D 67 TRP 0.008 0.001 TRP E 104 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.37 (19621) covalent geometry : angle 0.80318 / 0.45 (26628) SS BOND : bond 0.00065 / 0.05 ( 14) SS BOND : angle 0.65739 / 0.47 ( 28) hydrogen bonds : bond 0.13572 / 8.88 ( 1212) hydrogen bonds : angle 5.55503 / 3.95 ( 3552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.710 Fit side-chains REVERT: A 29 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8250 (mmt90) REVERT: A 57 GLU cc_start: 0.8556 (mp0) cc_final: 0.8099 (mp0) REVERT: A 337 GLU cc_start: 0.9110 (tp30) cc_final: 0.8532 (tm-30) REVERT: A 352 GLU cc_start: 0.9312 (tt0) cc_final: 0.9020 (tm-30) REVERT: B 9 GLU cc_start: 0.8521 (tt0) cc_final: 0.8214 (tt0) REVERT: B 29 ARG cc_start: 0.8685 (mmt-90) cc_final: 0.7842 (mmt-90) REVERT: B 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 57 GLU cc_start: 0.8776 (mp0) cc_final: 0.8258 (mp0) REVERT: B 337 GLU cc_start: 0.9058 (tp30) cc_final: 0.8360 (tm-30) REVERT: B 352 GLU cc_start: 0.9250 (tt0) cc_final: 0.8895 (tm-30) REVERT: C 9 GLU cc_start: 0.8523 (tt0) cc_final: 0.8198 (tt0) REVERT: C 29 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8016 (mmt-90) REVERT: C 57 GLU cc_start: 0.8724 (mp0) cc_final: 0.8313 (mp0) REVERT: C 128 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8471 (ttp80) REVERT: C 337 GLU cc_start: 0.9061 (tp30) cc_final: 0.8362 (tm-30) REVERT: C 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.8951 (tm-30) REVERT: D 9 GLU cc_start: 0.8477 (tt0) cc_final: 0.8188 (tt0) REVERT: D 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7976 (mmt-90) REVERT: D 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 337 GLU cc_start: 0.9121 (tp30) cc_final: 0.8399 (tm-30) REVERT: D 352 GLU cc_start: 0.9321 (tt0) cc_final: 0.8963 (tm-30) REVERT: E 9 GLU cc_start: 0.8563 (tt0) cc_final: 0.8270 (tt0) REVERT: E 29 ARG cc_start: 0.8723 (mmt-90) cc_final: 0.7903 (mmt-90) REVERT: E 57 GLU cc_start: 0.8767 (mp0) cc_final: 0.8266 (mp0) REVERT: E 128 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8524 (ttp80) REVERT: E 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8429 (tm-30) REVERT: E 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.9004 (tm-30) REVERT: F 9 GLU cc_start: 0.8553 (tt0) cc_final: 0.8241 (tt0) REVERT: F 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7906 (mmt-90) REVERT: F 31 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8262 (mt-10) REVERT: F 337 GLU cc_start: 0.9115 (tp30) cc_final: 0.8297 (tm-30) REVERT: F 352 GLU cc_start: 0.9285 (tt0) cc_final: 0.8942 (tm-30) REVERT: G 9 GLU cc_start: 0.8490 (tt0) cc_final: 0.8051 (tt0) REVERT: G 29 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.7887 (mmt-90) REVERT: G 31 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 57 GLU cc_start: 0.8731 (mp0) cc_final: 0.8429 (mp0) REVERT: G 337 GLU cc_start: 0.9102 (tp30) cc_final: 0.8420 (tm-30) REVERT: G 352 GLU cc_start: 0.9294 (tt0) cc_final: 0.8999 (tm-30) outliers start: 14 outliers final: 0 residues processed: 194 average time/residue: 0.7555 time to fit residues: 162.1508 Evaluate side-chains 113 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 208 ASN B 76 GLN B 208 ASN B 274 GLN C 76 GLN D 76 GLN D 208 ASN E 76 GLN E 208 ASN F 76 GLN F 208 ASN G 76 GLN G 208 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057357 restraints weight = 56535.246| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.04 r_work: 0.2909 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19635 Z= 0.129 Angle : 0.573 6.960 26656 Z= 0.286 Chirality : 0.039 0.123 3157 Planarity : 0.004 0.031 3115 Dihedral : 16.378 134.399 3325 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.16 % Allowed : 16.96 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2359 helix: 1.03 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 152 TYR 0.012 0.001 TYR A 345 PHE 0.007 0.001 PHE B 12 TRP 0.012 0.001 TRP B 104 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19621) covalent geometry : angle 0.57310 / 0.29 (26628) SS BOND : bond 0.00177 / 0.11 ( 14) SS BOND : angle 0.35839 / 0.25 ( 28) hydrogen bonds : bond 0.03970 / 2.64 ( 1212) hydrogen bonds : angle 4.37013 / 3.15 ( 3552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.630 Fit side-chains REVERT: A 5 GLN cc_start: 0.8106 (mp10) cc_final: 0.7661 (mp10) REVERT: A 9 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 29 ARG cc_start: 0.8798 (mmt-90) cc_final: 0.8184 (mmm-85) REVERT: A 138 ASP cc_start: 0.8715 (m-30) cc_final: 0.8310 (t0) REVERT: A 337 GLU cc_start: 0.9250 (tp30) cc_final: 0.8602 (tm-30) REVERT: A 352 GLU cc_start: 0.9415 (tt0) cc_final: 0.9165 (tm-30) REVERT: B 9 GLU cc_start: 0.8796 (tt0) cc_final: 0.8518 (tt0) REVERT: B 29 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8152 (mmt-90) REVERT: B 337 GLU cc_start: 0.9211 (tp30) cc_final: 0.8466 (tm-30) REVERT: B 352 GLU cc_start: 0.9376 (tt0) cc_final: 0.9083 (tm-30) REVERT: C 9 GLU cc_start: 0.8806 (tt0) cc_final: 0.8521 (tt0) REVERT: C 29 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8087 (mmt-90) REVERT: C 57 GLU cc_start: 0.8867 (mp0) cc_final: 0.8454 (mp0) REVERT: C 128 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8675 (ttp80) REVERT: C 337 GLU cc_start: 0.9207 (tp30) cc_final: 0.8455 (tm-30) REVERT: C 352 GLU cc_start: 0.9389 (tt0) cc_final: 0.9091 (tm-30) REVERT: D 9 GLU cc_start: 0.8771 (tt0) cc_final: 0.8506 (tt0) REVERT: D 29 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.7992 (mmt-90) REVERT: D 57 GLU cc_start: 0.8985 (mp0) cc_final: 0.8753 (mt-10) REVERT: D 337 GLU cc_start: 0.9194 (tp30) cc_final: 0.8437 (tm-30) REVERT: D 352 GLU cc_start: 0.9401 (tt0) cc_final: 0.9097 (tm-30) REVERT: E 9 GLU cc_start: 0.8777 (tt0) cc_final: 0.8467 (tt0) REVERT: E 29 ARG cc_start: 0.8706 (mmt-90) cc_final: 0.8049 (mmt-90) REVERT: E 128 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8718 (ttp80) REVERT: E 337 GLU cc_start: 0.9212 (tp30) cc_final: 0.8418 (tm-30) REVERT: E 352 GLU cc_start: 0.9379 (tt0) cc_final: 0.9112 (tm-30) REVERT: F 9 GLU cc_start: 0.8788 (tt0) cc_final: 0.8504 (tt0) REVERT: F 29 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.8222 (mmt-90) REVERT: F 57 GLU cc_start: 0.8826 (mp0) cc_final: 0.8355 (mp0) REVERT: F 337 GLU cc_start: 0.9233 (tp30) cc_final: 0.8497 (tm-30) REVERT: F 352 GLU cc_start: 0.9377 (tt0) cc_final: 0.9095 (tm-30) REVERT: G 9 GLU cc_start: 0.8693 (tt0) cc_final: 0.8355 (tt0) REVERT: G 29 ARG cc_start: 0.8645 (mmt-90) cc_final: 0.8006 (mmt-90) REVERT: G 57 GLU cc_start: 0.8881 (mp0) cc_final: 0.8461 (pm20) REVERT: G 337 GLU cc_start: 0.9229 (tp30) cc_final: 0.8391 (tm-30) REVERT: G 352 GLU cc_start: 0.9390 (tt0) cc_final: 0.9144 (tm-30) outliers start: 38 outliers final: 16 residues processed: 189 average time/residue: 0.7045 time to fit residues: 147.9961 Evaluate side-chains 127 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 159 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN A 274 GLN C 208 ASN C 274 GLN D 274 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.077276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054761 restraints weight = 58651.517| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.08 r_work: 0.2829 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 19635 Z= 0.235 Angle : 0.624 6.700 26656 Z= 0.309 Chirality : 0.041 0.131 3157 Planarity : 0.004 0.032 3115 Dihedral : 12.872 89.628 3325 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.67 % Allowed : 15.99 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2359 helix: 1.59 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 152 TYR 0.014 0.002 TYR A 10 PHE 0.015 0.001 PHE D 67 TRP 0.013 0.001 TRP C 104 HIS 0.002 0.001 HIS F 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (19621) covalent geometry : angle 0.62405 / 0.31 (26628) SS BOND : bond 0.00362 / 0.23 ( 14) SS BOND : angle 0.59756 / 0.42 ( 28) hydrogen bonds : bond 0.04222 / 2.83 ( 1212) hydrogen bonds : angle 4.40031 / 3.18 ( 3552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 109 time to evaluate : 0.720 Fit side-chains REVERT: A 5 GLN cc_start: 0.8431 (mp10) cc_final: 0.7896 (mp10) REVERT: A 9 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 29 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8182 (mmt-90) REVERT: A 337 GLU cc_start: 0.9195 (tp30) cc_final: 0.8509 (tm-30) REVERT: A 352 GLU cc_start: 0.9442 (tt0) cc_final: 0.9227 (tm-30) REVERT: B 5 GLN cc_start: 0.8297 (mp10) cc_final: 0.8059 (mp10) REVERT: B 9 GLU cc_start: 0.8735 (tt0) cc_final: 0.8447 (tt0) REVERT: B 29 ARG cc_start: 0.8746 (mmt-90) cc_final: 0.7958 (mmt-90) REVERT: B 89 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: B 337 GLU cc_start: 0.9169 (tp30) cc_final: 0.8243 (tm-30) REVERT: B 352 GLU cc_start: 0.9408 (tt0) cc_final: 0.9193 (tm-30) REVERT: C 9 GLU cc_start: 0.8773 (tt0) cc_final: 0.8488 (tt0) REVERT: C 29 ARG cc_start: 0.8747 (mmt-90) cc_final: 0.8198 (mmt-90) REVERT: C 57 GLU cc_start: 0.8812 (mp0) cc_final: 0.8467 (mp0) REVERT: C 128 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8758 (ttp80) REVERT: C 337 GLU cc_start: 0.9150 (tp30) cc_final: 0.8423 (tm-30) REVERT: C 352 GLU cc_start: 0.9436 (tt0) cc_final: 0.9192 (tm-30) REVERT: D 9 GLU cc_start: 0.8695 (tt0) cc_final: 0.8438 (tt0) REVERT: D 29 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.7769 (mmt-90) REVERT: D 57 GLU cc_start: 0.9007 (mp0) cc_final: 0.8595 (mp0) REVERT: D 337 GLU cc_start: 0.9111 (tp30) cc_final: 0.8229 (tm-30) REVERT: D 352 GLU cc_start: 0.9424 (tt0) cc_final: 0.9171 (tm-30) REVERT: E 9 GLU cc_start: 0.8776 (tt0) cc_final: 0.8503 (tt0) REVERT: E 29 ARG cc_start: 0.8748 (mmt-90) cc_final: 0.8029 (mmt-90) REVERT: E 128 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8755 (ttp80) REVERT: E 337 GLU cc_start: 0.9150 (tp30) cc_final: 0.8366 (tm-30) REVERT: E 352 GLU cc_start: 0.9395 (tt0) cc_final: 0.9169 (tm-30) REVERT: F 9 GLU cc_start: 0.8778 (tt0) cc_final: 0.8478 (tt0) REVERT: F 29 ARG cc_start: 0.8751 (mmt-90) cc_final: 0.8162 (mmt-90) REVERT: F 57 GLU cc_start: 0.8788 (mp0) cc_final: 0.8359 (mp0) REVERT: F 337 GLU cc_start: 0.9115 (tp30) cc_final: 0.8380 (tm-30) REVERT: F 352 GLU cc_start: 0.9425 (tt0) cc_final: 0.9165 (tm-30) REVERT: G 5 GLN cc_start: 0.8391 (mp10) cc_final: 0.8145 (mp10) REVERT: G 9 GLU cc_start: 0.8612 (tt0) cc_final: 0.8303 (tt0) REVERT: G 29 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.7911 (mmt-90) REVERT: G 57 GLU cc_start: 0.8798 (mp0) cc_final: 0.8423 (mt-10) REVERT: G 337 GLU cc_start: 0.9126 (tp30) cc_final: 0.8236 (tm-30) REVERT: G 352 GLU cc_start: 0.9420 (tt0) cc_final: 0.9209 (tm-30) outliers start: 82 outliers final: 29 residues processed: 189 average time/residue: 0.5866 time to fit residues: 125.5865 Evaluate side-chains 134 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 282 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056045 restraints weight = 57669.794| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.06 r_work: 0.2871 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19635 Z= 0.162 Angle : 0.550 7.186 26656 Z= 0.274 Chirality : 0.039 0.122 3157 Planarity : 0.004 0.035 3115 Dihedral : 11.868 92.389 3325 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.30 % Allowed : 17.93 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2359 helix: 1.92 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.74 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 152 TYR 0.011 0.001 TYR A 345 PHE 0.009 0.001 PHE D 67 TRP 0.013 0.001 TRP C 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19621) covalent geometry : angle 0.55036 / 0.27 (26628) SS BOND : bond 0.00231 / 0.15 ( 14) SS BOND : angle 0.41229 / 0.30 ( 28) hydrogen bonds : bond 0.03623 / 2.42 ( 1212) hydrogen bonds : angle 4.21390 / 3.05 ( 3552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 116 time to evaluate : 0.741 Fit side-chains REVERT: A 5 GLN cc_start: 0.8451 (mp10) cc_final: 0.7877 (mp10) REVERT: A 9 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 29 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8049 (mmm-85) REVERT: A 57 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: A 336 GLU cc_start: 0.8924 (tt0) cc_final: 0.8706 (mt-10) REVERT: A 337 GLU cc_start: 0.9195 (tp30) cc_final: 0.8502 (tm-30) REVERT: B 5 GLN cc_start: 0.8284 (mp10) cc_final: 0.8045 (mp10) REVERT: B 9 GLU cc_start: 0.8737 (tt0) cc_final: 0.8483 (tt0) REVERT: B 29 ARG cc_start: 0.8671 (mmt-90) cc_final: 0.8068 (mmt-90) REVERT: B 31 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8615 (mm-30) REVERT: B 57 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: B 152 ARG cc_start: 0.8932 (tmm-80) cc_final: 0.8660 (ttp80) REVERT: B 337 GLU cc_start: 0.9169 (tp30) cc_final: 0.8338 (tm-30) REVERT: C 9 GLU cc_start: 0.8704 (tt0) cc_final: 0.8421 (tt0) REVERT: C 29 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.7994 (mmt-90) REVERT: C 57 GLU cc_start: 0.8816 (mp0) cc_final: 0.8592 (mp0) REVERT: C 128 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8731 (ttp80) REVERT: C 147 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8905 (p0) REVERT: C 337 GLU cc_start: 0.9146 (tp30) cc_final: 0.8406 (tm-30) REVERT: C 352 GLU cc_start: 0.9422 (tt0) cc_final: 0.9198 (tm-30) REVERT: D 9 GLU cc_start: 0.8719 (tt0) cc_final: 0.8469 (tt0) REVERT: D 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.7867 (mmt-90) REVERT: D 31 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8570 (mm-30) REVERT: D 337 GLU cc_start: 0.9115 (tp30) cc_final: 0.8330 (tm-30) REVERT: D 352 GLU cc_start: 0.9442 (tt0) cc_final: 0.9230 (tm-30) REVERT: E 9 GLU cc_start: 0.8738 (tt0) cc_final: 0.8458 (tt0) REVERT: E 29 ARG cc_start: 0.8722 (mmt-90) cc_final: 0.8116 (mmt-90) REVERT: E 57 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8628 (pm20) REVERT: E 128 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8739 (ttp80) REVERT: E 147 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8884 (p0) REVERT: E 337 GLU cc_start: 0.9132 (tp30) cc_final: 0.8376 (tm-30) REVERT: F 9 GLU cc_start: 0.8729 (tt0) cc_final: 0.8468 (tt0) REVERT: F 29 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.8096 (mmt-90) REVERT: F 31 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8517 (mm-30) REVERT: F 57 GLU cc_start: 0.8793 (mp0) cc_final: 0.8405 (mp0) REVERT: F 147 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8970 (p0) REVERT: F 337 GLU cc_start: 0.9099 (tp30) cc_final: 0.8317 (tm-30) REVERT: F 352 GLU cc_start: 0.9413 (tt0) cc_final: 0.9180 (tm-30) REVERT: G 5 GLN cc_start: 0.8455 (mp10) cc_final: 0.8197 (mp10) REVERT: G 9 GLU cc_start: 0.8594 (tt0) cc_final: 0.8306 (tt0) REVERT: G 29 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.7794 (mmt-90) REVERT: G 31 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8638 (mm-30) REVERT: G 57 GLU cc_start: 0.8723 (mp0) cc_final: 0.8340 (mt-10) REVERT: G 147 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8941 (p0) REVERT: G 337 GLU cc_start: 0.9088 (tp30) cc_final: 0.8207 (tm-30) outliers start: 58 outliers final: 26 residues processed: 171 average time/residue: 0.7225 time to fit residues: 137.7510 Evaluate side-chains 139 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057510 restraints weight = 56979.190| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.08 r_work: 0.2911 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19635 Z= 0.115 Angle : 0.550 8.141 26656 Z= 0.267 Chirality : 0.038 0.110 3157 Planarity : 0.004 0.065 3115 Dihedral : 11.198 84.634 3325 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.28 % Allowed : 20.89 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 2359 helix: 2.08 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 254 TYR 0.011 0.001 TYR B 345 PHE 0.009 0.001 PHE G 109 TRP 0.013 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (19621) covalent geometry : angle 0.55013 / 0.27 (26628) SS BOND : bond 0.00124 / 0.08 ( 14) SS BOND : angle 0.33781 / 0.24 ( 28) hydrogen bonds : bond 0.03337 / 2.23 ( 1212) hydrogen bonds : angle 4.07422 / 2.95 ( 3552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.784 Fit side-chains REVERT: A 5 GLN cc_start: 0.8440 (mp10) cc_final: 0.7903 (mp10) REVERT: A 29 ARG cc_start: 0.8693 (mmt-90) cc_final: 0.8003 (mmm-85) REVERT: A 337 GLU cc_start: 0.9188 (tp30) cc_final: 0.8523 (tm-30) REVERT: B 5 GLN cc_start: 0.8351 (mp10) cc_final: 0.8086 (mp10) REVERT: B 9 GLU cc_start: 0.8766 (tt0) cc_final: 0.8504 (tt0) REVERT: B 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8018 (mmt-90) REVERT: B 57 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8828 (pm20) REVERT: B 152 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8617 (ttp80) REVERT: B 337 GLU cc_start: 0.9172 (tp30) cc_final: 0.8355 (tm-30) REVERT: C 5 GLN cc_start: 0.8310 (mp10) cc_final: 0.8086 (pm20) REVERT: C 9 GLU cc_start: 0.8745 (tt0) cc_final: 0.8474 (tt0) REVERT: C 29 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.7993 (mmt-90) REVERT: C 128 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8742 (ttp80) REVERT: C 147 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8898 (p0) REVERT: C 337 GLU cc_start: 0.9147 (tp30) cc_final: 0.8407 (tm-30) REVERT: C 352 GLU cc_start: 0.9421 (tt0) cc_final: 0.9186 (tm-30) REVERT: D 9 GLU cc_start: 0.8717 (tt0) cc_final: 0.8475 (tt0) REVERT: D 29 ARG cc_start: 0.8584 (mmt-90) cc_final: 0.7942 (mmt-90) REVERT: D 31 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8516 (mm-30) REVERT: D 337 GLU cc_start: 0.9086 (tp30) cc_final: 0.8376 (tm-30) REVERT: D 352 GLU cc_start: 0.9435 (tt0) cc_final: 0.9211 (tm-30) REVERT: E 9 GLU cc_start: 0.8737 (tt0) cc_final: 0.8481 (tt0) REVERT: E 29 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.7936 (mmt-90) REVERT: E 57 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: E 128 ARG cc_start: 0.9086 (ttp80) cc_final: 0.8717 (ttp80) REVERT: E 147 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8884 (p0) REVERT: E 337 GLU cc_start: 0.9090 (tp30) cc_final: 0.8292 (tm-30) REVERT: F 9 GLU cc_start: 0.8708 (tt0) cc_final: 0.8453 (tt0) REVERT: F 29 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.7970 (mmt-90) REVERT: F 147 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8950 (p0) REVERT: F 337 GLU cc_start: 0.9091 (tp30) cc_final: 0.8327 (tm-30) REVERT: F 352 GLU cc_start: 0.9405 (tt0) cc_final: 0.9168 (tm-30) REVERT: G 5 GLN cc_start: 0.8474 (mp10) cc_final: 0.8186 (mp10) REVERT: G 9 GLU cc_start: 0.8598 (tt0) cc_final: 0.8365 (tt0) REVERT: G 29 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.7844 (mmt-90) REVERT: G 57 GLU cc_start: 0.8674 (mp0) cc_final: 0.8409 (mt-10) REVERT: G 147 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8933 (p0) REVERT: G 337 GLU cc_start: 0.9090 (tp30) cc_final: 0.8246 (tm-30) outliers start: 40 outliers final: 21 residues processed: 154 average time/residue: 0.7450 time to fit residues: 127.5563 Evaluate side-chains 130 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 71 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 96 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 30.0000 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 GLN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.079680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057721 restraints weight = 57139.923| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.11 r_work: 0.2918 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19635 Z= 0.118 Angle : 0.545 7.153 26656 Z= 0.267 Chirality : 0.038 0.114 3157 Planarity : 0.004 0.038 3115 Dihedral : 10.594 74.902 3325 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.56 % Allowed : 21.57 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2359 helix: 2.18 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 254 TYR 0.010 0.001 TYR A 345 PHE 0.006 0.001 PHE E 263 TRP 0.010 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19621) covalent geometry : angle 0.54477 / 0.27 (26628) SS BOND : bond 0.00129 / 0.08 ( 14) SS BOND : angle 0.34025 / 0.25 ( 28) hydrogen bonds : bond 0.03240 / 2.16 ( 1212) hydrogen bonds : angle 4.01095 / 2.90 ( 3552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.652 Fit side-chains REVERT: A 5 GLN cc_start: 0.8349 (mp10) cc_final: 0.8067 (mp10) REVERT: A 29 ARG cc_start: 0.8680 (mmt-90) cc_final: 0.8025 (mmt-90) REVERT: A 337 GLU cc_start: 0.9192 (tp30) cc_final: 0.8474 (tm-30) REVERT: B 5 GLN cc_start: 0.8374 (mp10) cc_final: 0.8086 (mp10) REVERT: B 9 GLU cc_start: 0.8768 (tt0) cc_final: 0.8482 (tt0) REVERT: B 29 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8007 (mmt-90) REVERT: B 152 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8599 (ttp80) REVERT: B 337 GLU cc_start: 0.9137 (tp30) cc_final: 0.8328 (tm-30) REVERT: C 9 GLU cc_start: 0.8719 (tt0) cc_final: 0.8464 (tt0) REVERT: C 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.7871 (mmt-90) REVERT: C 128 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8747 (ttp80) REVERT: C 337 GLU cc_start: 0.9151 (tp30) cc_final: 0.8377 (tm-30) REVERT: C 352 GLU cc_start: 0.9438 (tt0) cc_final: 0.9192 (tm-30) REVERT: D 29 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.7853 (mmt-90) REVERT: D 337 GLU cc_start: 0.9083 (tp30) cc_final: 0.8323 (tm-30) REVERT: D 352 GLU cc_start: 0.9428 (tt0) cc_final: 0.9221 (tm-30) REVERT: E 9 GLU cc_start: 0.8690 (tt0) cc_final: 0.8454 (tt0) REVERT: E 29 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.7965 (mmt-90) REVERT: E 57 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: E 128 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8720 (ttp80) REVERT: E 147 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8862 (p0) REVERT: E 337 GLU cc_start: 0.9094 (tp30) cc_final: 0.8288 (tm-30) REVERT: F 9 GLU cc_start: 0.8704 (tt0) cc_final: 0.8458 (tt0) REVERT: F 29 ARG cc_start: 0.8635 (mmt-90) cc_final: 0.8032 (mmt-90) REVERT: F 147 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8962 (p0) REVERT: F 152 ARG cc_start: 0.8928 (tmm-80) cc_final: 0.8609 (ttp80) REVERT: F 337 GLU cc_start: 0.9090 (tp30) cc_final: 0.8355 (tm-30) REVERT: F 352 GLU cc_start: 0.9416 (tt0) cc_final: 0.9189 (tm-30) REVERT: G 5 GLN cc_start: 0.8482 (mp10) cc_final: 0.8188 (mp10) REVERT: G 9 GLU cc_start: 0.8585 (tt0) cc_final: 0.8330 (tt0) REVERT: G 29 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.7785 (mmt-90) REVERT: G 31 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8075 (mm-30) REVERT: G 57 GLU cc_start: 0.8667 (mp0) cc_final: 0.8308 (mt-10) REVERT: G 147 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (p0) REVERT: G 337 GLU cc_start: 0.9108 (tp30) cc_final: 0.8244 (tm-30) outliers start: 45 outliers final: 26 residues processed: 154 average time/residue: 0.6950 time to fit residues: 119.1744 Evaluate side-chains 129 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 228 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055454 restraints weight = 58039.835| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.15 r_work: 0.2853 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19635 Z= 0.171 Angle : 0.574 7.187 26656 Z= 0.284 Chirality : 0.039 0.124 3157 Planarity : 0.004 0.037 3115 Dihedral : 10.464 69.261 3325 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.79 % Allowed : 21.12 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2359 helix: 2.18 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 254 TYR 0.010 0.001 TYR A 345 PHE 0.010 0.001 PHE A 67 TRP 0.009 0.001 TRP G 104 HIS 0.001 0.000 HIS F 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (19621) covalent geometry : angle 0.57391 / 0.28 (26628) SS BOND : bond 0.00227 / 0.15 ( 14) SS BOND : angle 0.46892 / 0.34 ( 28) hydrogen bonds : bond 0.03540 / 2.36 ( 1212) hydrogen bonds : angle 4.09230 / 2.95 ( 3552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.723 Fit side-chains REVERT: A 5 GLN cc_start: 0.8541 (mp10) cc_final: 0.8069 (mp10) REVERT: A 29 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.8087 (mmt-90) REVERT: A 337 GLU cc_start: 0.9166 (tp30) cc_final: 0.8533 (tm-30) REVERT: B 5 GLN cc_start: 0.8350 (mp10) cc_final: 0.8082 (mp10) REVERT: B 9 GLU cc_start: 0.8755 (tt0) cc_final: 0.8528 (tt0) REVERT: B 29 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.7979 (mmt-90) REVERT: B 89 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8713 (mt0) REVERT: B 152 ARG cc_start: 0.8908 (tmm-80) cc_final: 0.8608 (ttp80) REVERT: B 337 GLU cc_start: 0.9139 (tp30) cc_final: 0.8263 (tm-30) REVERT: C 9 GLU cc_start: 0.8709 (tt0) cc_final: 0.8449 (tt0) REVERT: C 29 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.7967 (mmt-90) REVERT: C 128 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8772 (ttp80) REVERT: C 337 GLU cc_start: 0.9113 (tp30) cc_final: 0.8356 (tm-30) REVERT: C 352 GLU cc_start: 0.9448 (tt0) cc_final: 0.9218 (tm-30) REVERT: D 29 ARG cc_start: 0.8627 (mmt-90) cc_final: 0.7974 (mmt-90) REVERT: D 337 GLU cc_start: 0.9103 (tp30) cc_final: 0.8393 (tm-30) REVERT: D 352 GLU cc_start: 0.9448 (tt0) cc_final: 0.9227 (tm-30) REVERT: E 9 GLU cc_start: 0.8689 (tt0) cc_final: 0.8457 (tt0) REVERT: E 29 ARG cc_start: 0.8674 (mmt-90) cc_final: 0.7883 (mmt-90) REVERT: E 57 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: E 89 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8703 (mt0) REVERT: E 128 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8719 (ttp80) REVERT: E 337 GLU cc_start: 0.9072 (tp30) cc_final: 0.8281 (tm-30) REVERT: F 9 GLU cc_start: 0.8683 (tt0) cc_final: 0.8444 (tt0) REVERT: F 29 ARG cc_start: 0.8650 (mmt-90) cc_final: 0.8053 (mmt-90) REVERT: F 152 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8606 (ttp80) REVERT: F 337 GLU cc_start: 0.9064 (tp30) cc_final: 0.8322 (tm-30) REVERT: F 352 GLU cc_start: 0.9430 (tt0) cc_final: 0.9211 (tm-30) REVERT: G 5 GLN cc_start: 0.8476 (mp10) cc_final: 0.8172 (mp10) REVERT: G 9 GLU cc_start: 0.8593 (tt0) cc_final: 0.8308 (tt0) REVERT: G 29 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.7948 (mmt-90) REVERT: G 31 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8105 (mm-30) REVERT: G 57 GLU cc_start: 0.8735 (mp0) cc_final: 0.8513 (mp0) REVERT: G 337 GLU cc_start: 0.9091 (tp30) cc_final: 0.8255 (tm-30) outliers start: 49 outliers final: 30 residues processed: 150 average time/residue: 0.7300 time to fit residues: 121.7631 Evaluate side-chains 130 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 40 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.078914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056935 restraints weight = 57240.996| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.15 r_work: 0.2890 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19635 Z= 0.119 Angle : 0.549 7.269 26656 Z= 0.273 Chirality : 0.038 0.111 3157 Planarity : 0.004 0.037 3115 Dihedral : 10.003 66.307 3325 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.33 % Allowed : 21.68 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 2359 helix: 2.21 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.010 0.001 TYR B 345 PHE 0.008 0.001 PHE E 54 TRP 0.012 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19621) covalent geometry : angle 0.54928 / 0.27 (26628) SS BOND : bond 0.00128 / 0.08 ( 14) SS BOND : angle 0.34339 / 0.25 ( 28) hydrogen bonds : bond 0.03238 / 2.16 ( 1212) hydrogen bonds : angle 4.00185 / 2.89 ( 3552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.767 Fit side-chains REVERT: A 5 GLN cc_start: 0.8501 (mp10) cc_final: 0.8090 (mp10) REVERT: A 29 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.7961 (mmt-90) REVERT: A 337 GLU cc_start: 0.9173 (tp30) cc_final: 0.8475 (tm-30) REVERT: B 5 GLN cc_start: 0.8318 (mp10) cc_final: 0.8065 (mp10) REVERT: B 9 GLU cc_start: 0.8773 (tt0) cc_final: 0.8504 (tt0) REVERT: B 29 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8087 (mmt-90) REVERT: B 152 ARG cc_start: 0.8914 (tmm-80) cc_final: 0.8597 (ttp80) REVERT: B 337 GLU cc_start: 0.9127 (tp30) cc_final: 0.8346 (tm-30) REVERT: C 9 GLU cc_start: 0.8725 (tt0) cc_final: 0.8501 (tt0) REVERT: C 29 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.7935 (mmt-90) REVERT: C 128 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8736 (ttp80) REVERT: C 337 GLU cc_start: 0.9120 (tp30) cc_final: 0.8364 (tm-30) REVERT: C 352 GLU cc_start: 0.9446 (tt0) cc_final: 0.9208 (tm-30) REVERT: D 29 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.7939 (mmt-90) REVERT: D 337 GLU cc_start: 0.9066 (tp30) cc_final: 0.8301 (tm-30) REVERT: E 9 GLU cc_start: 0.8669 (tt0) cc_final: 0.8450 (tt0) REVERT: E 29 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.7942 (mmt-90) REVERT: E 57 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8607 (pm20) REVERT: E 128 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8709 (ttp80) REVERT: E 337 GLU cc_start: 0.9084 (tp30) cc_final: 0.8301 (tm-30) REVERT: F 9 GLU cc_start: 0.8685 (tt0) cc_final: 0.8460 (tt0) REVERT: F 29 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8089 (mmt-90) REVERT: F 152 ARG cc_start: 0.8916 (tmm-80) cc_final: 0.8642 (ttp80) REVERT: F 337 GLU cc_start: 0.9057 (tp30) cc_final: 0.8334 (tm-30) REVERT: F 352 GLU cc_start: 0.9420 (tt0) cc_final: 0.9206 (tm-30) REVERT: G 5 GLN cc_start: 0.8478 (mp10) cc_final: 0.8162 (mp10) REVERT: G 9 GLU cc_start: 0.8593 (tt0) cc_final: 0.8337 (tt0) REVERT: G 29 ARG cc_start: 0.8600 (mmt-90) cc_final: 0.7922 (mmt-90) REVERT: G 31 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8121 (mm-30) REVERT: G 57 GLU cc_start: 0.8720 (mp0) cc_final: 0.8500 (mp0) REVERT: G 337 GLU cc_start: 0.9072 (tp30) cc_final: 0.8249 (tm-30) outliers start: 41 outliers final: 28 residues processed: 143 average time/residue: 0.7419 time to fit residues: 117.7010 Evaluate side-chains 125 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 116 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 188 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 174 optimal weight: 0.0070 chunk 169 optimal weight: 0.0980 chunk 15 optimal weight: 20.0000 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.080885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059103 restraints weight = 57333.099| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.19 r_work: 0.2956 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19635 Z= 0.103 Angle : 0.545 8.989 26656 Z= 0.271 Chirality : 0.037 0.107 3157 Planarity : 0.004 0.066 3115 Dihedral : 9.160 61.628 3325 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.71 % Allowed : 22.54 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2359 helix: 2.32 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 254 TYR 0.010 0.001 TYR D 345 PHE 0.010 0.001 PHE B 54 TRP 0.014 0.001 TRP F 104 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (19621) covalent geometry : angle 0.54563 / 0.27 (26628) SS BOND : bond 0.00070 / 0.04 ( 14) SS BOND : angle 0.21568 / 0.16 ( 28) hydrogen bonds : bond 0.02792 / 1.86 ( 1212) hydrogen bonds : angle 3.87801 / 2.80 ( 3552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.729 Fit side-chains REVERT: A 5 GLN cc_start: 0.8456 (mp10) cc_final: 0.8085 (mp10) REVERT: A 29 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.7996 (mmt-90) REVERT: A 337 GLU cc_start: 0.9183 (tp30) cc_final: 0.8436 (tm-30) REVERT: B 5 GLN cc_start: 0.8297 (mp10) cc_final: 0.8052 (mp10) REVERT: B 9 GLU cc_start: 0.8723 (tt0) cc_final: 0.8439 (tt0) REVERT: B 29 ARG cc_start: 0.8594 (mmt-90) cc_final: 0.8031 (mmt-90) REVERT: B 152 ARG cc_start: 0.8887 (tmm-80) cc_final: 0.8627 (ttp80) REVERT: B 337 GLU cc_start: 0.9149 (tp30) cc_final: 0.8352 (tm-30) REVERT: C 9 GLU cc_start: 0.8713 (tt0) cc_final: 0.8502 (tt0) REVERT: C 29 ARG cc_start: 0.8595 (mmt-90) cc_final: 0.7946 (mmt-90) REVERT: C 128 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8664 (ttp80) REVERT: C 337 GLU cc_start: 0.9129 (tp30) cc_final: 0.8337 (tm-30) REVERT: C 352 GLU cc_start: 0.9419 (tt0) cc_final: 0.9190 (tm-30) REVERT: D 29 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.7928 (mmt-90) REVERT: D 337 GLU cc_start: 0.9065 (tp30) cc_final: 0.8328 (tm-30) REVERT: E 29 ARG cc_start: 0.8509 (mmt-90) cc_final: 0.7965 (mmt-90) REVERT: E 57 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: E 128 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8712 (ttp80) REVERT: E 337 GLU cc_start: 0.9065 (tp30) cc_final: 0.8279 (tm-30) REVERT: F 9 GLU cc_start: 0.8697 (tt0) cc_final: 0.8468 (tt0) REVERT: F 29 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.8084 (mmt-90) REVERT: F 152 ARG cc_start: 0.8877 (tmm-80) cc_final: 0.8611 (ttp80) REVERT: F 337 GLU cc_start: 0.9071 (tp30) cc_final: 0.8340 (tm-30) REVERT: F 352 GLU cc_start: 0.9400 (tt0) cc_final: 0.9167 (tm-30) REVERT: G 5 GLN cc_start: 0.8466 (mp10) cc_final: 0.8165 (mp10) REVERT: G 9 GLU cc_start: 0.8642 (tt0) cc_final: 0.8403 (tt0) REVERT: G 29 ARG cc_start: 0.8502 (mmt-90) cc_final: 0.7808 (mmt-90) REVERT: G 31 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8065 (mm-30) REVERT: G 57 GLU cc_start: 0.8644 (mp0) cc_final: 0.8213 (mt-10) REVERT: G 254 ARG cc_start: 0.9230 (ttm110) cc_final: 0.8981 (ttm110) REVERT: G 337 GLU cc_start: 0.9071 (tp30) cc_final: 0.8198 (tm-30) outliers start: 30 outliers final: 15 residues processed: 137 average time/residue: 0.7638 time to fit residues: 115.9939 Evaluate side-chains 115 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN F 89 GLN G 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.080405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058503 restraints weight = 57824.480| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.20 r_work: 0.2941 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19635 Z= 0.108 Angle : 0.544 7.782 26656 Z= 0.271 Chirality : 0.037 0.112 3157 Planarity : 0.004 0.081 3115 Dihedral : 8.909 59.711 3325 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.31 % Allowed : 22.88 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 2359 helix: 2.38 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 254 TYR 0.009 0.001 TYR A 345 PHE 0.010 0.001 PHE F 244 TRP 0.009 0.001 TRP C 104 HIS 0.001 0.000 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19621) covalent geometry : angle 0.54444 / 0.27 (26628) SS BOND : bond 0.00112 / 0.08 ( 14) SS BOND : angle 0.31614 / 0.23 ( 28) hydrogen bonds : bond 0.02892 / 1.92 ( 1212) hydrogen bonds : angle 3.77579 / 2.73 ( 3552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.802 Fit side-chains REVERT: A 5 GLN cc_start: 0.8459 (mp10) cc_final: 0.8060 (mp10) REVERT: A 29 ARG cc_start: 0.8594 (mmt-90) cc_final: 0.7994 (mmt-90) REVERT: A 337 GLU cc_start: 0.9184 (tp30) cc_final: 0.8401 (tm-30) REVERT: B 5 GLN cc_start: 0.8338 (mp10) cc_final: 0.8100 (mp10) REVERT: B 9 GLU cc_start: 0.8731 (tt0) cc_final: 0.8473 (tt0) REVERT: B 29 ARG cc_start: 0.8605 (mmt-90) cc_final: 0.8051 (mmt-90) REVERT: B 152 ARG cc_start: 0.8873 (tmm-80) cc_final: 0.8621 (ttp80) REVERT: B 337 GLU cc_start: 0.9146 (tp30) cc_final: 0.8340 (tm-30) REVERT: C 9 GLU cc_start: 0.8731 (tt0) cc_final: 0.8513 (tt0) REVERT: C 29 ARG cc_start: 0.8606 (mmt-90) cc_final: 0.7955 (mmt-90) REVERT: C 128 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8675 (ttp80) REVERT: C 337 GLU cc_start: 0.9135 (tp30) cc_final: 0.8380 (tm-30) REVERT: C 352 GLU cc_start: 0.9426 (tt0) cc_final: 0.9184 (tm-30) REVERT: D 29 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.7975 (mmt-90) REVERT: D 337 GLU cc_start: 0.9071 (tp30) cc_final: 0.8307 (tm-30) REVERT: E 29 ARG cc_start: 0.8534 (mmt-90) cc_final: 0.7903 (mmt-90) REVERT: E 57 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: E 128 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8721 (ttp80) REVERT: E 337 GLU cc_start: 0.9069 (tp30) cc_final: 0.8193 (tm-30) REVERT: F 9 GLU cc_start: 0.8728 (tt0) cc_final: 0.8494 (tt0) REVERT: F 29 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.7997 (mmt-90) REVERT: F 152 ARG cc_start: 0.8847 (tmm-80) cc_final: 0.8566 (ttp80) REVERT: F 337 GLU cc_start: 0.9085 (tp30) cc_final: 0.8292 (tm-30) REVERT: F 352 GLU cc_start: 0.9401 (tt0) cc_final: 0.9158 (tm-30) REVERT: G 5 GLN cc_start: 0.8459 (mp10) cc_final: 0.8146 (mp10) REVERT: G 9 GLU cc_start: 0.8675 (tt0) cc_final: 0.8439 (tt0) REVERT: G 29 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.7786 (mmt-90) REVERT: G 31 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8056 (mm-30) REVERT: G 57 GLU cc_start: 0.8665 (mp0) cc_final: 0.8159 (mt-10) REVERT: G 337 GLU cc_start: 0.9068 (tp30) cc_final: 0.8194 (tm-30) outliers start: 23 outliers final: 14 residues processed: 124 average time/residue: 0.7995 time to fit residues: 109.4225 Evaluate side-chains 115 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 199 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 49 optimal weight: 30.0000 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.080531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058688 restraints weight = 57776.962| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.19 r_work: 0.2945 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19635 Z= 0.107 Angle : 0.540 7.987 26656 Z= 0.269 Chirality : 0.037 0.116 3157 Planarity : 0.004 0.079 3115 Dihedral : 8.705 57.984 3325 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.31 % Allowed : 22.88 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 2359 helix: 2.40 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.55 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 254 TYR 0.009 0.001 TYR C 345 PHE 0.007 0.001 PHE E 54 TRP 0.010 0.001 TRP G 104 HIS 0.001 0.000 HIS F 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (19621) covalent geometry : angle 0.54063 / 0.27 (26628) SS BOND : bond 0.00116 / 0.08 ( 14) SS BOND : angle 0.34877 / 0.25 ( 28) hydrogen bonds : bond 0.02864 / 1.90 ( 1212) hydrogen bonds : angle 3.73430 / 2.70 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.52 seconds wall clock time: 87 minutes 49.35 seconds (5269.35 seconds total)