Starting phenix.real_space_refine on Thu Mar 5 06:44:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbm_21593/03_2026/6wbm_21593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbm_21593/03_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_21593/03_2026/6wbm_21593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbm_21593/03_2026/6wbm_21593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbm_21593/03_2026/6wbm_21593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbm_21593/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.88, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.54 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: 3.23 Time building geometry restraints manager: 2.56 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: 12054 31.50 - 63.00: 539 63.00 - 94.50: 28 94.50 - 125.99: 0 125.99 - 157.49: 21 Dihedral angle restraints: 12642 sinusoidal: 5537 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 12639 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: 2.000 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.440 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 17.310 157.493 7980 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 covalent geometry : bond 0.00681 (19621) covalent geometry : angle 0.80318 (26628) SS BOND : bond 0.00065 ( 14) SS BOND : angle 0.65739 ( 28) hydrogen bonds : bond 0.13572 ( 1212) hydrogen bonds : angle 5.55503 ( 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 : 0.695 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: 0.7763 time to fit residues: 165.7740 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 : 0.780 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 208 ASN B 76 GLN B 208 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.079623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057470 restraints weight = 56612.772| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.04 r_work: 0.2913 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19635 Z= 0.129 Angle : 0.573 6.981 26656 Z= 0.284 Chirality : 0.039 0.130 3157 Planarity : 0.004 0.031 3115 Dihedral : 15.709 136.829 4347 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 16.90 % Favored : 80.82 % 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: 0.19 (0.18), residues: 2359 helix: 1.09 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.09 (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 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00288 (19621) covalent geometry : angle 0.57320 (26628) SS BOND : bond 0.00172 ( 14) SS BOND : angle 0.38033 ( 28) hydrogen bonds : bond 0.03888 ( 1212) hydrogen bonds : angle 4.34096 ( 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 205 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.728 Fit side-chains REVERT: A 5 GLN cc_start: 0.8123 (mp10) cc_final: 0.7674 (mp10) REVERT: A 9 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 29 ARG cc_start: 0.8786 (mmt-90) cc_final: 0.8159 (mmm-85) REVERT: A 138 ASP cc_start: 0.8717 (m-30) cc_final: 0.8322 (t0) REVERT: A 337 GLU cc_start: 0.9247 (tp30) cc_final: 0.8596 (tm-30) REVERT: A 352 GLU cc_start: 0.9417 (tt0) cc_final: 0.9161 (tm-30) REVERT: B 9 GLU cc_start: 0.8798 (tt0) cc_final: 0.8517 (tt0) REVERT: B 29 ARG cc_start: 0.8653 (mmt-90) cc_final: 0.8166 (mmt-90) REVERT: B 337 GLU cc_start: 0.9211 (tp30) cc_final: 0.8459 (tm-30) REVERT: B 352 GLU cc_start: 0.9386 (tt0) cc_final: 0.9114 (tm-30) REVERT: C 9 GLU cc_start: 0.8806 (tt0) cc_final: 0.8507 (tt0) REVERT: C 29 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8024 (mmt-90) REVERT: C 57 GLU cc_start: 0.8884 (mp0) cc_final: 0.8471 (mp0) REVERT: C 128 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8668 (ttp80) REVERT: C 337 GLU cc_start: 0.9207 (tp30) cc_final: 0.8404 (tm-30) REVERT: C 352 GLU cc_start: 0.9391 (tt0) cc_final: 0.9106 (tm-30) REVERT: D 9 GLU cc_start: 0.8771 (tt0) cc_final: 0.8503 (tt0) REVERT: D 29 ARG cc_start: 0.8617 (mmt-90) cc_final: 0.7985 (mmt-90) REVERT: D 57 GLU cc_start: 0.8981 (mp0) cc_final: 0.8758 (mt-10) REVERT: D 337 GLU cc_start: 0.9190 (tp30) cc_final: 0.8429 (tm-30) REVERT: D 352 GLU cc_start: 0.9402 (tt0) cc_final: 0.9108 (tm-30) REVERT: E 9 GLU cc_start: 0.8776 (tt0) cc_final: 0.8461 (tt0) REVERT: E 29 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8056 (mmt-90) REVERT: E 128 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8710 (ttp80) REVERT: E 337 GLU cc_start: 0.9217 (tp30) cc_final: 0.8450 (tm-30) REVERT: E 352 GLU cc_start: 0.9378 (tt0) cc_final: 0.9115 (tm-30) REVERT: F 9 GLU cc_start: 0.8785 (tt0) cc_final: 0.8498 (tt0) REVERT: F 29 ARG cc_start: 0.8637 (mmt-90) cc_final: 0.8209 (mmt-90) REVERT: F 337 GLU cc_start: 0.9230 (tp30) cc_final: 0.8488 (tm-30) REVERT: F 352 GLU cc_start: 0.9380 (tt0) cc_final: 0.9100 (tm-30) REVERT: G 9 GLU cc_start: 0.8692 (tt0) cc_final: 0.8365 (tt0) REVERT: G 29 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.8004 (mmt-90) REVERT: G 57 GLU cc_start: 0.8884 (mp0) cc_final: 0.8456 (pm20) REVERT: G 337 GLU cc_start: 0.9230 (tp30) cc_final: 0.8385 (tm-30) REVERT: G 352 GLU cc_start: 0.9394 (tt0) cc_final: 0.9149 (tm-30) outliers start: 40 outliers final: 19 residues processed: 197 average time/residue: 0.7596 time to fit residues: 165.0162 Evaluate side-chains 128 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 225 LEU 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 37 MET 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 37 MET 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: 1.9990 chunk 181 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 101 optimal weight: 0.0170 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: 20.0000 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN C 89 GLN C 208 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.078673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056285 restraints weight = 58113.475| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.10 r_work: 0.2880 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19635 Z= 0.158 Angle : 0.568 6.670 26656 Z= 0.280 Chirality : 0.039 0.117 3157 Planarity : 0.004 0.040 3115 Dihedral : 13.166 92.846 4347 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.93 % Allowed : 16.33 % Favored : 79.74 % 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: 1.02 (0.18), residues: 2359 helix: 1.74 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 152 TYR 0.012 0.001 TYR B 345 PHE 0.009 0.001 PHE D 67 TRP 0.012 0.001 TRP G 104 HIS 0.002 0.000 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00371 (19621) covalent geometry : angle 0.56857 (26628) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.42825 ( 28) hydrogen bonds : bond 0.03752 ( 1212) hydrogen bonds : angle 4.23412 ( 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 181 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 112 time to evaluate : 0.738 Fit side-chains REVERT: A 5 GLN cc_start: 0.8376 (mp10) cc_final: 0.7867 (mp10) REVERT: A 29 ARG cc_start: 0.8757 (mmt-90) cc_final: 0.8225 (mmt-90) REVERT: A 336 GLU cc_start: 0.8912 (tt0) cc_final: 0.8691 (tt0) REVERT: A 337 GLU cc_start: 0.9182 (tp30) cc_final: 0.8525 (tm-30) REVERT: A 352 GLU cc_start: 0.9434 (tt0) cc_final: 0.9227 (tm-30) REVERT: B 9 GLU cc_start: 0.8745 (tt0) cc_final: 0.8469 (tt0) REVERT: B 29 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8018 (mmt-90) REVERT: B 89 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8725 (mt0) REVERT: B 337 GLU cc_start: 0.9177 (tp30) cc_final: 0.8366 (tm-30) REVERT: B 352 GLU cc_start: 0.9408 (tt0) cc_final: 0.9182 (tm-30) REVERT: C 9 GLU cc_start: 0.8780 (tt0) cc_final: 0.8497 (tt0) REVERT: C 29 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8017 (mmt-90) REVERT: C 128 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8758 (ttp80) REVERT: C 337 GLU cc_start: 0.9171 (tp30) cc_final: 0.8351 (tm-30) REVERT: C 352 GLU cc_start: 0.9424 (tt0) cc_final: 0.9172 (tm-30) REVERT: D 9 GLU cc_start: 0.8716 (tt0) cc_final: 0.8467 (tt0) REVERT: D 29 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.7793 (mmt-90) REVERT: D 57 GLU cc_start: 0.8937 (mp0) cc_final: 0.8560 (mp0) REVERT: D 337 GLU cc_start: 0.9124 (tp30) cc_final: 0.8342 (tm-30) REVERT: D 352 GLU cc_start: 0.9413 (tt0) cc_final: 0.9168 (tm-30) REVERT: E 9 GLU cc_start: 0.8755 (tt0) cc_final: 0.8444 (tt0) REVERT: E 29 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.7917 (mmt-90) REVERT: E 128 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8727 (ttp80) REVERT: E 336 GLU cc_start: 0.9033 (tt0) cc_final: 0.8806 (mt-10) REVERT: E 337 GLU cc_start: 0.9166 (tp30) cc_final: 0.8341 (tm-30) REVERT: E 352 GLU cc_start: 0.9393 (tt0) cc_final: 0.9173 (tm-30) REVERT: F 9 GLU cc_start: 0.8792 (tt0) cc_final: 0.8533 (tt0) REVERT: F 29 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: F 337 GLU cc_start: 0.9133 (tp30) cc_final: 0.8352 (tm-30) REVERT: F 352 GLU cc_start: 0.9409 (tt0) cc_final: 0.9152 (tm-30) REVERT: G 5 GLN cc_start: 0.8331 (mp10) cc_final: 0.8120 (mp10) REVERT: G 9 GLU cc_start: 0.8611 (tt0) cc_final: 0.8305 (tt0) REVERT: G 29 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.7826 (mmt-90) REVERT: G 57 GLU cc_start: 0.8759 (mp0) cc_final: 0.8487 (mp0) REVERT: G 336 GLU cc_start: 0.8948 (tt0) cc_final: 0.8741 (mt-10) REVERT: G 337 GLU cc_start: 0.9123 (tp30) cc_final: 0.8248 (tm-30) REVERT: G 352 GLU cc_start: 0.9415 (tt0) cc_final: 0.9193 (tm-30) outliers start: 69 outliers final: 23 residues processed: 180 average time/residue: 0.6627 time to fit residues: 133.6779 Evaluate side-chains 132 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS 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 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 89 GLN 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 209 LEU 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 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 225 LEU Chi-restraints excluded: chain F residue 246 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 43 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN B 274 GLN D 89 GLN G 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057475 restraints weight = 57333.425| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.07 r_work: 0.2914 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2128 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= 0.116 Angle : 0.532 7.145 26656 Z= 0.263 Chirality : 0.038 0.109 3157 Planarity : 0.004 0.035 3115 Dihedral : 12.316 90.815 4347 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.07 % Allowed : 17.93 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2359 helix: 1.97 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 152 TYR 0.011 0.001 TYR A 345 PHE 0.009 0.001 PHE C 109 TRP 0.014 0.001 TRP C 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00263 (19621) covalent geometry : angle 0.53263 (26628) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.34665 ( 28) hydrogen bonds : bond 0.03387 ( 1212) hydrogen bonds : angle 4.09487 ( 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 170 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.764 Fit side-chains REVERT: A 5 GLN cc_start: 0.8303 (mp10) cc_final: 0.7876 (mp10) REVERT: A 29 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8046 (mmt-90) REVERT: A 57 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (pm20) REVERT: A 337 GLU cc_start: 0.9198 (tp30) cc_final: 0.8459 (tm-30) REVERT: B 9 GLU cc_start: 0.8756 (tt0) cc_final: 0.8499 (tt0) REVERT: B 29 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8080 (mmt-90) REVERT: B 31 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 152 ARG cc_start: 0.8887 (tmm-80) cc_final: 0.8618 (ttp80) REVERT: B 337 GLU cc_start: 0.9157 (tp30) cc_final: 0.8401 (tm-30) REVERT: C 9 GLU cc_start: 0.8769 (tt0) cc_final: 0.8513 (tt0) REVERT: C 29 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8112 (mmt-90) REVERT: C 128 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8725 (ttp80) REVERT: C 337 GLU cc_start: 0.9153 (tp30) cc_final: 0.8381 (tm-30) REVERT: C 352 GLU cc_start: 0.9414 (tt0) cc_final: 0.9185 (tm-30) REVERT: D 9 GLU cc_start: 0.8707 (tt0) cc_final: 0.8462 (tt0) REVERT: D 29 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.7906 (mmt-90) REVERT: D 31 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8479 (mm-30) REVERT: D 337 GLU cc_start: 0.9096 (tp30) cc_final: 0.8331 (tm-30) REVERT: D 352 GLU cc_start: 0.9416 (tt0) cc_final: 0.9176 (tm-30) REVERT: E 9 GLU cc_start: 0.8745 (tt0) cc_final: 0.8478 (tt0) REVERT: E 29 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8038 (mmt-90) REVERT: E 57 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: E 128 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8717 (ttp80) REVERT: E 337 GLU cc_start: 0.9159 (tp30) cc_final: 0.8338 (tm-30) REVERT: E 352 GLU cc_start: 0.9395 (tt0) cc_final: 0.9187 (tm-30) REVERT: F 9 GLU cc_start: 0.8734 (tt0) cc_final: 0.8486 (tt0) REVERT: F 29 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.7937 (mmt-90) REVERT: F 31 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8480 (mm-30) REVERT: F 147 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8961 (p0) REVERT: F 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8257 (tm-30) REVERT: F 352 GLU cc_start: 0.9399 (tt0) cc_final: 0.9165 (tm-30) REVERT: G 9 GLU cc_start: 0.8604 (tt0) cc_final: 0.8329 (tt0) REVERT: G 29 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.7825 (mmt-90) REVERT: G 31 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8630 (mm-30) REVERT: G 57 GLU cc_start: 0.8704 (mp0) cc_final: 0.8457 (mp0) REVERT: G 337 GLU cc_start: 0.9108 (tp30) cc_final: 0.8237 (tm-30) outliers start: 54 outliers final: 26 residues processed: 167 average time/residue: 0.7594 time to fit residues: 140.9544 Evaluate side-chains 136 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 225 LEU 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 3 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE 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 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 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 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 130 optimal weight: 0.0030 chunk 195 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 232 optimal weight: 0.0070 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.079438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057399 restraints weight = 57209.969| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.10 r_work: 0.2914 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19635 Z= 0.124 Angle : 0.552 8.005 26656 Z= 0.267 Chirality : 0.038 0.117 3157 Planarity : 0.004 0.036 3115 Dihedral : 11.873 84.373 4347 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 19.75 % Favored : 77.75 % 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: 1.51 (0.19), residues: 2359 helix: 2.12 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 152 TYR 0.011 0.001 TYR B 345 PHE 0.007 0.001 PHE G 109 TRP 0.011 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00284 (19621) covalent geometry : angle 0.55180 (26628) SS BOND : bond 0.00147 ( 14) SS BOND : angle 0.35931 ( 28) hydrogen bonds : bond 0.03333 ( 1212) hydrogen bonds : angle 4.05435 ( 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: 44 poor density : 112 time to evaluate : 0.719 Fit side-chains REVERT: A 5 GLN cc_start: 0.8261 (mp10) cc_final: 0.7851 (mp10) REVERT: A 29 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8029 (mmt-90) REVERT: A 337 GLU cc_start: 0.9189 (tp30) cc_final: 0.8442 (tm-30) REVERT: B 9 GLU cc_start: 0.8781 (tt0) cc_final: 0.8548 (tt0) REVERT: B 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8043 (mmt-90) REVERT: B 31 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8571 (mm-30) REVERT: B 152 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8609 (ttp80) REVERT: B 337 GLU cc_start: 0.9156 (tp30) cc_final: 0.8397 (tm-30) REVERT: C 9 GLU cc_start: 0.8759 (tt0) cc_final: 0.8505 (tt0) REVERT: C 29 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.7971 (mmt-90) REVERT: C 128 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8746 (ttp80) REVERT: C 337 GLU cc_start: 0.9150 (tp30) cc_final: 0.8354 (tm-30) REVERT: C 352 GLU cc_start: 0.9422 (tt0) cc_final: 0.9189 (tm-30) REVERT: D 9 GLU cc_start: 0.8691 (tt0) cc_final: 0.8450 (tt0) REVERT: D 29 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.7877 (mmt-90) REVERT: D 31 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8459 (mm-30) REVERT: D 337 GLU cc_start: 0.9093 (tp30) cc_final: 0.8326 (tm-30) REVERT: D 352 GLU cc_start: 0.9432 (tt0) cc_final: 0.9189 (tm-30) REVERT: E 9 GLU cc_start: 0.8725 (tt0) cc_final: 0.8480 (tt0) REVERT: E 29 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.8006 (mmt-90) REVERT: E 89 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8703 (mt0) REVERT: E 128 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8715 (ttp80) REVERT: E 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8291 (tm-30) REVERT: E 352 GLU cc_start: 0.9399 (tt0) cc_final: 0.9177 (tm-30) REVERT: F 9 GLU cc_start: 0.8735 (tt0) cc_final: 0.8494 (tt0) REVERT: F 29 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.8048 (mmt-90) REVERT: F 147 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8953 (p0) REVERT: F 337 GLU cc_start: 0.9091 (tp30) cc_final: 0.8294 (tm-30) REVERT: F 352 GLU cc_start: 0.9402 (tt0) cc_final: 0.9164 (tm-30) REVERT: G 9 GLU cc_start: 0.8620 (tt0) cc_final: 0.8362 (tt0) REVERT: G 29 ARG cc_start: 0.8522 (mmt-90) cc_final: 0.7815 (mmt-90) REVERT: G 57 GLU cc_start: 0.8636 (mp0) cc_final: 0.8421 (mp0) REVERT: G 89 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: G 337 GLU cc_start: 0.9068 (tp30) cc_final: 0.8216 (tm-30) outliers start: 44 outliers final: 22 residues processed: 152 average time/residue: 0.7894 time to fit residues: 132.5641 Evaluate side-chains 128 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 225 LEU 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 211 ILE 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 89 GLN 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 209 LEU 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 209 LEU Chi-restraints excluded: chain G residue 211 ILE 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: 9.9990 chunk 203 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 0.0170 chunk 128 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 89 GLN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.078780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056665 restraints weight = 57406.604| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.11 r_work: 0.2893 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19635 Z= 0.156 Angle : 0.564 7.246 26656 Z= 0.276 Chirality : 0.038 0.119 3157 Planarity : 0.004 0.036 3115 Dihedral : 11.583 75.203 4347 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.13 % Allowed : 19.92 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.56 (0.19), residues: 2359 helix: 2.16 (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 0.003 0.000 ARG D 152 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 A 134 Details of bonding type rmsd covalent geometry : bond 0.00366 (19621) covalent geometry : angle 0.56431 (26628) SS BOND : bond 0.00209 ( 14) SS BOND : angle 0.42663 ( 28) hydrogen bonds : bond 0.03481 ( 1212) hydrogen bonds : angle 4.07883 ( 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: 55 poor density : 101 time to evaluate : 0.712 Fit side-chains REVERT: A 5 GLN cc_start: 0.8317 (mp10) cc_final: 0.7896 (mp10) REVERT: A 29 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8041 (mmt-90) REVERT: A 337 GLU cc_start: 0.9172 (tp30) cc_final: 0.8440 (tm-30) REVERT: B 9 GLU cc_start: 0.8759 (tt0) cc_final: 0.8535 (tt0) REVERT: B 29 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.8000 (mmt-90) REVERT: B 31 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8598 (mm-30) REVERT: B 152 ARG cc_start: 0.8891 (tmm-80) cc_final: 0.8595 (ttp80) REVERT: B 337 GLU cc_start: 0.9146 (tp30) cc_final: 0.8346 (tm-30) REVERT: C 9 GLU cc_start: 0.8730 (tt0) cc_final: 0.8478 (tt0) REVERT: C 29 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.7917 (mmt-90) REVERT: C 128 ARG cc_start: 0.9071 (ttp80) cc_final: 0.8762 (ttp80) REVERT: C 337 GLU cc_start: 0.9137 (tp30) cc_final: 0.8327 (tm-30) REVERT: C 352 GLU cc_start: 0.9434 (tt0) cc_final: 0.9195 (tm-30) REVERT: D 9 GLU cc_start: 0.8684 (tt0) cc_final: 0.8453 (tt0) REVERT: D 29 ARG cc_start: 0.8583 (mmt-90) cc_final: 0.7850 (mmt-90) REVERT: D 31 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8466 (mm-30) REVERT: D 337 GLU cc_start: 0.9099 (tp30) cc_final: 0.8336 (tm-30) REVERT: D 352 GLU cc_start: 0.9437 (tt0) cc_final: 0.9200 (tm-30) REVERT: E 9 GLU cc_start: 0.8722 (tt0) cc_final: 0.8464 (tt0) REVERT: E 29 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.7942 (mmt-90) REVERT: E 89 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8787 (mt0) REVERT: E 128 ARG cc_start: 0.9071 (ttp80) cc_final: 0.8712 (ttp80) REVERT: E 337 GLU cc_start: 0.9078 (tp30) cc_final: 0.8225 (tm-30) REVERT: E 352 GLU cc_start: 0.9403 (tt0) cc_final: 0.9190 (tm-30) REVERT: F 9 GLU cc_start: 0.8719 (tt0) cc_final: 0.8496 (tt0) REVERT: F 29 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8152 (mmt-90) REVERT: F 147 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8961 (p0) REVERT: F 152 ARG cc_start: 0.8919 (tmm-80) cc_final: 0.8603 (ttp80) REVERT: F 337 GLU cc_start: 0.9078 (tp30) cc_final: 0.8406 (tm-30) REVERT: F 352 GLU cc_start: 0.9423 (tt0) cc_final: 0.9186 (tm-30) REVERT: G 9 GLU cc_start: 0.8621 (tt0) cc_final: 0.8363 (tt0) REVERT: G 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.7898 (mmt-90) REVERT: G 31 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8071 (mm-30) REVERT: G 57 GLU cc_start: 0.8684 (mp0) cc_final: 0.8123 (mp0) REVERT: G 337 GLU cc_start: 0.9089 (tp30) cc_final: 0.8270 (tm-30) outliers start: 55 outliers final: 30 residues processed: 154 average time/residue: 0.7500 time to fit residues: 128.2977 Evaluate side-chains 129 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS 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 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 D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE 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 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 195 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 228 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 206 optimal weight: 0.0470 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056149 restraints weight = 57791.579| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.10 r_work: 0.2878 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2378 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= 0.170 Angle : 0.573 7.188 26656 Z= 0.281 Chirality : 0.039 0.124 3157 Planarity : 0.004 0.036 3115 Dihedral : 11.436 71.191 4347 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.62 % Allowed : 20.26 % Favored : 77.12 % 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: 1.58 (0.19), residues: 2359 helix: 2.16 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.010 0.001 TYR D 345 PHE 0.011 0.001 PHE A 67 TRP 0.009 0.001 TRP C 104 HIS 0.001 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00400 (19621) covalent geometry : angle 0.57311 (26628) SS BOND : bond 0.00240 ( 14) SS BOND : angle 0.45206 ( 28) hydrogen bonds : bond 0.03551 ( 1212) hydrogen bonds : angle 4.09966 ( 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 148 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.762 Fit side-chains REVERT: A 5 GLN cc_start: 0.8291 (mp10) cc_final: 0.7880 (mp10) REVERT: A 29 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.7978 (mmm-85) REVERT: A 337 GLU cc_start: 0.9173 (tp30) cc_final: 0.8509 (tm-30) REVERT: B 9 GLU cc_start: 0.8753 (tt0) cc_final: 0.8525 (tt0) REVERT: B 29 ARG cc_start: 0.8651 (mmt-90) cc_final: 0.7995 (mmt-90) REVERT: B 31 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8618 (mm-30) REVERT: B 152 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8601 (ttp80) REVERT: B 337 GLU cc_start: 0.9144 (tp30) cc_final: 0.8345 (tm-30) REVERT: C 9 GLU cc_start: 0.8717 (tt0) cc_final: 0.8468 (tt0) REVERT: C 29 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.7920 (mmt-90) REVERT: C 128 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8775 (ttp80) REVERT: C 337 GLU cc_start: 0.9126 (tp30) cc_final: 0.8315 (tm-30) REVERT: C 352 GLU cc_start: 0.9446 (tt0) cc_final: 0.9195 (tm-30) REVERT: D 9 GLU cc_start: 0.8694 (tt0) cc_final: 0.8469 (tt0) REVERT: D 29 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.7873 (mmt-90) REVERT: D 31 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8470 (mm-30) REVERT: D 337 GLU cc_start: 0.9095 (tp30) cc_final: 0.8332 (tm-30) REVERT: D 352 GLU cc_start: 0.9455 (tt0) cc_final: 0.9223 (tm-30) REVERT: E 9 GLU cc_start: 0.8721 (tt0) cc_final: 0.8477 (tt0) REVERT: E 29 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.7950 (mmt-90) REVERT: E 128 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8725 (ttp80) REVERT: E 337 GLU cc_start: 0.9065 (tp30) cc_final: 0.8299 (tm-30) REVERT: E 352 GLU cc_start: 0.9412 (tt0) cc_final: 0.9179 (tm-30) REVERT: F 9 GLU cc_start: 0.8714 (tt0) cc_final: 0.8470 (tt0) REVERT: F 29 ARG cc_start: 0.8661 (mmt-90) cc_final: 0.7993 (mmt-90) REVERT: F 147 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8961 (p0) REVERT: F 152 ARG cc_start: 0.8917 (tmm-80) cc_final: 0.8605 (ttp80) REVERT: F 337 GLU cc_start: 0.9096 (tp30) cc_final: 0.8338 (tm-30) REVERT: F 352 GLU cc_start: 0.9427 (tt0) cc_final: 0.9188 (tm-30) REVERT: G 9 GLU cc_start: 0.8628 (tt0) cc_final: 0.8379 (tt0) REVERT: G 29 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.7922 (mmt-90) REVERT: G 31 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8121 (mm-30) REVERT: G 89 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: G 337 GLU cc_start: 0.9093 (tp30) cc_final: 0.8270 (tm-30) outliers start: 46 outliers final: 32 residues processed: 146 average time/residue: 0.7820 time to fit residues: 126.4192 Evaluate side-chains 129 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 224 ILE Chi-restraints excluded: chain A residue 246 CYS 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 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 282 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE 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 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 F residue 282 VAL Chi-restraints excluded: chain G residue 89 GLN 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 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: 3.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 GLN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.077260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055124 restraints weight = 57626.888| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.12 r_work: 0.2845 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2435 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= 0.179 Angle : 0.589 7.191 26656 Z= 0.291 Chirality : 0.039 0.125 3157 Planarity : 0.004 0.088 3115 Dihedral : 11.284 74.025 4347 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 20.60 % Favored : 76.89 % 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: 1.56 (0.19), residues: 2359 helix: 2.15 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 254 TYR 0.011 0.001 TYR A 10 PHE 0.011 0.001 PHE F 67 TRP 0.010 0.001 TRP C 104 HIS 0.001 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00421 (19621) covalent geometry : angle 0.58920 (26628) SS BOND : bond 0.00257 ( 14) SS BOND : angle 0.47293 ( 28) hydrogen bonds : bond 0.03641 ( 1212) hydrogen bonds : angle 4.12114 ( 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 144 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.714 Fit side-chains REVERT: A 5 GLN cc_start: 0.8286 (mp10) cc_final: 0.7878 (mp10) REVERT: A 29 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.8086 (mmt-90) REVERT: A 337 GLU cc_start: 0.9170 (tp30) cc_final: 0.8521 (tm-30) REVERT: B 9 GLU cc_start: 0.8737 (tt0) cc_final: 0.8515 (tt0) REVERT: B 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.7976 (mmt-90) REVERT: B 31 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8577 (mm-30) REVERT: B 152 ARG cc_start: 0.8903 (tmm-80) cc_final: 0.8599 (ttp80) REVERT: B 337 GLU cc_start: 0.9142 (tp30) cc_final: 0.8289 (tm-30) REVERT: C 9 GLU cc_start: 0.8698 (tt0) cc_final: 0.8451 (tt0) REVERT: C 29 ARG cc_start: 0.8691 (mmt-90) cc_final: 0.7971 (mmt-90) REVERT: C 128 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8768 (ttp80) REVERT: C 337 GLU cc_start: 0.9101 (tp30) cc_final: 0.8348 (tm-30) REVERT: C 352 GLU cc_start: 0.9439 (tt0) cc_final: 0.9211 (tm-30) REVERT: D 9 GLU cc_start: 0.8687 (tt0) cc_final: 0.8460 (tt0) REVERT: D 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.7966 (mmt-90) REVERT: D 31 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8452 (mm-30) REVERT: D 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8440 (tm-30) REVERT: D 352 GLU cc_start: 0.9455 (tt0) cc_final: 0.9231 (tm-30) REVERT: E 9 GLU cc_start: 0.8705 (tt0) cc_final: 0.8461 (tt0) REVERT: E 29 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: E 128 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8717 (ttp80) REVERT: E 337 GLU cc_start: 0.9077 (tp30) cc_final: 0.8290 (tm-30) REVERT: E 352 GLU cc_start: 0.9418 (tt0) cc_final: 0.9199 (tm-30) REVERT: F 9 GLU cc_start: 0.8680 (tt0) cc_final: 0.8430 (tt0) REVERT: F 29 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.8085 (mmt-90) REVERT: F 147 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8961 (p0) REVERT: F 152 ARG cc_start: 0.8916 (tmm-80) cc_final: 0.8606 (ttp80) REVERT: F 337 GLU cc_start: 0.9084 (tp30) cc_final: 0.8343 (tm-30) REVERT: F 352 GLU cc_start: 0.9430 (tt0) cc_final: 0.9194 (tm-30) REVERT: G 9 GLU cc_start: 0.8642 (tt0) cc_final: 0.8403 (tt0) REVERT: G 29 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8056 (mmt-90) REVERT: G 31 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8178 (mm-30) REVERT: G 337 GLU cc_start: 0.9062 (tp30) cc_final: 0.8282 (tm-30) outliers start: 44 outliers final: 31 residues processed: 142 average time/residue: 0.7831 time to fit residues: 123.3022 Evaluate side-chains 125 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 225 LEU 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 282 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS 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 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 F residue 282 VAL Chi-restraints excluded: chain G residue 89 GLN 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 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: 20.0000 chunk 103 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 174 optimal weight: 0.9990 chunk 169 optimal weight: 0.0370 chunk 15 optimal weight: 8.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.079498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057621 restraints weight = 56860.750| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.15 r_work: 0.2915 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2728 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= 0.109 Angle : 0.555 7.970 26656 Z= 0.275 Chirality : 0.037 0.138 3157 Planarity : 0.004 0.070 3115 Dihedral : 10.747 82.355 4347 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.82 % Allowed : 21.74 % Favored : 76.44 % 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: 1.70 (0.19), residues: 2359 helix: 2.25 (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 0.018 0.001 ARG G 254 TYR 0.010 0.001 TYR A 10 PHE 0.011 0.001 PHE F 54 TRP 0.014 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00240 (19621) covalent geometry : angle 0.55536 (26628) SS BOND : bond 0.00104 ( 14) SS BOND : angle 0.28574 ( 28) hydrogen bonds : bond 0.03085 ( 1212) hydrogen bonds : angle 3.95716 ( 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: 32 poor density : 107 time to evaluate : 0.744 Fit side-chains REVERT: A 5 GLN cc_start: 0.8189 (mp10) cc_final: 0.7857 (mp10) REVERT: A 29 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.7930 (mmt-90) REVERT: A 337 GLU cc_start: 0.9182 (tp30) cc_final: 0.8441 (tm-30) REVERT: B 9 GLU cc_start: 0.8782 (tt0) cc_final: 0.8547 (tt0) REVERT: B 29 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8023 (mmt-90) REVERT: B 31 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8501 (mm-30) REVERT: B 152 ARG cc_start: 0.8909 (tmm-80) cc_final: 0.8591 (ttp80) REVERT: B 337 GLU cc_start: 0.9121 (tp30) cc_final: 0.8383 (tm-30) REVERT: C 9 GLU cc_start: 0.8740 (tt0) cc_final: 0.8530 (tt0) REVERT: C 29 ARG cc_start: 0.8577 (mmt-90) cc_final: 0.7830 (mmt-90) REVERT: C 128 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8746 (ttp80) REVERT: C 337 GLU cc_start: 0.9119 (tp30) cc_final: 0.8333 (tm-30) REVERT: C 352 GLU cc_start: 0.9424 (tt0) cc_final: 0.9192 (tm-30) REVERT: D 29 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.7887 (mmt-90) REVERT: D 31 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8412 (mm-30) REVERT: D 337 GLU cc_start: 0.9056 (tp30) cc_final: 0.8300 (tm-30) REVERT: D 352 GLU cc_start: 0.9435 (tt0) cc_final: 0.9217 (tm-30) REVERT: E 9 GLU cc_start: 0.8688 (tt0) cc_final: 0.8453 (tt0) REVERT: E 29 ARG cc_start: 0.8583 (mmt-90) cc_final: 0.7951 (mmt-90) REVERT: E 128 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8704 (ttp80) REVERT: E 337 GLU cc_start: 0.9052 (tp30) cc_final: 0.8281 (tm-30) REVERT: E 352 GLU cc_start: 0.9404 (tt0) cc_final: 0.9200 (tm-30) REVERT: F 9 GLU cc_start: 0.8691 (tt0) cc_final: 0.8464 (tt0) REVERT: F 29 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8030 (mmt-90) REVERT: F 31 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8216 (mm-30) REVERT: F 152 ARG cc_start: 0.8900 (tmm-80) cc_final: 0.8587 (ttp80) REVERT: F 337 GLU cc_start: 0.9086 (tp30) cc_final: 0.8328 (tm-30) REVERT: F 352 GLU cc_start: 0.9413 (tt0) cc_final: 0.9199 (tm-30) REVERT: G 9 GLU cc_start: 0.8669 (tt0) cc_final: 0.8444 (tt0) REVERT: G 29 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.7936 (mmt-90) REVERT: G 31 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8106 (mm-30) REVERT: G 337 GLU cc_start: 0.9050 (tp30) cc_final: 0.8225 (tm-30) outliers start: 32 outliers final: 20 residues processed: 139 average time/residue: 0.7418 time to fit residues: 114.4420 Evaluate side-chains 114 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 246 CYS 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 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 246 CYS 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 225 LEU Chi-restraints excluded: chain F residue 246 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 219 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 GLN F 89 GLN G 56 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.076986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.055200 restraints weight = 57944.675| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.12 r_work: 0.2847 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19635 Z= 0.197 Angle : 0.607 7.440 26656 Z= 0.301 Chirality : 0.039 0.126 3157 Planarity : 0.004 0.067 3115 Dihedral : 10.950 85.560 4347 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.59 % Allowed : 22.14 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2359 helix: 2.23 (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 0.017 0.001 ARG G 254 TYR 0.010 0.001 TYR D 10 PHE 0.012 0.001 PHE D 67 TRP 0.012 0.001 TRP A 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00465 (19621) covalent geometry : angle 0.60717 (26628) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.49247 ( 28) hydrogen bonds : bond 0.03659 ( 1212) hydrogen bonds : angle 4.10803 ( 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 124 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.709 Fit side-chains REVERT: A 5 GLN cc_start: 0.8283 (mp10) cc_final: 0.7897 (mp10) REVERT: A 29 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8034 (mmt-90) REVERT: A 337 GLU cc_start: 0.9175 (tp30) cc_final: 0.8534 (tm-30) REVERT: B 9 GLU cc_start: 0.8791 (tt0) cc_final: 0.8572 (tt0) REVERT: B 29 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.7955 (mmt-90) REVERT: B 31 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8524 (mm-30) REVERT: B 152 ARG cc_start: 0.8918 (tmm-80) cc_final: 0.8597 (ttp80) REVERT: B 337 GLU cc_start: 0.9143 (tp30) cc_final: 0.8331 (tm-30) REVERT: C 9 GLU cc_start: 0.8719 (tt0) cc_final: 0.8490 (tt0) REVERT: C 29 ARG cc_start: 0.8697 (mmt-90) cc_final: 0.7990 (mmt-90) REVERT: C 128 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8753 (ttp80) REVERT: C 337 GLU cc_start: 0.9117 (tp30) cc_final: 0.8361 (tm-30) REVERT: C 352 GLU cc_start: 0.9454 (tt0) cc_final: 0.9213 (tm-30) REVERT: D 29 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.7995 (mmt-90) REVERT: D 31 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8419 (mm-30) REVERT: D 337 GLU cc_start: 0.9106 (tp30) cc_final: 0.8454 (tm-30) REVERT: D 352 GLU cc_start: 0.9447 (tt0) cc_final: 0.9227 (tm-30) REVERT: E 9 GLU cc_start: 0.8697 (tt0) cc_final: 0.8459 (tt0) REVERT: E 29 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.7892 (mmt-90) REVERT: E 128 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8718 (ttp80) REVERT: E 337 GLU cc_start: 0.9076 (tp30) cc_final: 0.8296 (tm-30) REVERT: E 352 GLU cc_start: 0.9412 (tt0) cc_final: 0.9194 (tm-30) REVERT: F 9 GLU cc_start: 0.8704 (tt0) cc_final: 0.8476 (tt0) REVERT: F 29 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8100 (mmt-90) REVERT: F 31 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8279 (mm-30) REVERT: F 152 ARG cc_start: 0.8896 (tmm-80) cc_final: 0.8575 (ttp80) REVERT: F 337 GLU cc_start: 0.9078 (tp30) cc_final: 0.8338 (tm-30) REVERT: F 352 GLU cc_start: 0.9432 (tt0) cc_final: 0.9201 (tm-30) REVERT: G 9 GLU cc_start: 0.8643 (tt0) cc_final: 0.8436 (tt0) REVERT: G 29 ARG cc_start: 0.8671 (mmt-90) cc_final: 0.8057 (mmt-90) REVERT: G 31 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8134 (mm-30) REVERT: G 337 GLU cc_start: 0.9052 (tp30) cc_final: 0.8279 (tm-30) outliers start: 28 outliers final: 21 residues processed: 122 average time/residue: 0.7649 time to fit residues: 103.0949 Evaluate side-chains 114 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 246 CYS 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 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL 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 225 LEU Chi-restraints excluded: chain F residue 246 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 59 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 49 optimal weight: 30.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.077981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055993 restraints weight = 57458.601| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.13 r_work: 0.2873 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19635 Z= 0.143 Angle : 0.574 7.805 26656 Z= 0.285 Chirality : 0.038 0.120 3157 Planarity : 0.004 0.064 3115 Dihedral : 10.798 88.604 4347 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 22.25 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 2359 helix: 2.24 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 254 TYR 0.010 0.001 TYR A 10 PHE 0.009 0.001 PHE B 334 TRP 0.013 0.001 TRP A 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00338 (19621) covalent geometry : angle 0.57457 (26628) SS BOND : bond 0.00188 ( 14) SS BOND : angle 0.39155 ( 28) hydrogen bonds : bond 0.03403 ( 1212) hydrogen bonds : angle 4.03919 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.70 seconds wall clock time: 93 minutes 49.06 seconds (5629.06 seconds total)