Starting phenix.real_space_refine on Thu Feb 5 15:03:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hf3_52106/02_2026/9hf3_52106.map" } resolution = 2.45 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 11977 2.51 5 N 2723 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17920 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "B" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "C" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "D" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "E" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "F" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2487 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 3 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.82, per 1000 atoms: 0.21 Number of scatterers: 17920 At special positions: 0 Unit cell: (112.45, 113.1, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3136 8.00 N 2723 7.00 C 11977 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 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " 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: 1.44 Conformation dependent library (CDL) restraints added in 704.0 milliseconds 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4214 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 74.2% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.391A pdb=" N SER A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 100 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.515A pdb=" N LYS A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.745A pdb=" N LYS A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.972A pdb=" N ASN A 254 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.674A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.391A pdb=" N SER B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 100 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.516A pdb=" N LYS B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 3.746A pdb=" N LYS B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.972A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.673A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.391A pdb=" N SER C 92 " --> pdb=" O GLN C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 100 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 removed outlier: 3.516A pdb=" N LYS C 202 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 removed outlier: 3.745A pdb=" N LYS C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.973A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.674A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 341 through 357 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.537A 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 89 through 92 removed outlier: 6.392A pdb=" N SER D 92 " --> pdb=" O GLN D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 100 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 203 removed outlier: 3.515A pdb=" N LYS D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 removed outlier: 3.745A pdb=" N LYS D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.973A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.674A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 340 Processing helix chain 'D' and resid 341 through 357 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.392A pdb=" N SER E 92 " --> pdb=" O GLN E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 100 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 203 removed outlier: 3.515A pdb=" N LYS E 202 " --> pdb=" O TYR E 198 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 removed outlier: 3.746A pdb=" N LYS E 211 " --> pdb=" O HIS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.972A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.674A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 341 through 357 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.392A pdb=" N SER F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 100 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 3.516A pdb=" N LYS F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 removed outlier: 3.746A pdb=" N LYS F 211 " --> pdb=" O HIS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.972A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 299 removed outlier: 3.507A pdb=" N ILE F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.674A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 340 Processing helix chain 'F' and resid 341 through 357 Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.538A 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 89 through 92 removed outlier: 6.392A pdb=" N SER G 92 " --> pdb=" O GLN G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 100 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 161 removed outlier: 3.545A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 203 removed outlier: 3.515A pdb=" N LYS G 202 " --> pdb=" O TYR G 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 203 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 removed outlier: 3.746A pdb=" N LYS G 211 " --> pdb=" O HIS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.972A pdb=" N ASN G 254 " --> pdb=" O VAL G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 299 removed outlier: 3.506A pdb=" N ILE G 278 " --> pdb=" O LEU G 274 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.674A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Proline residue: G 297 - end of helix Processing helix chain 'G' and resid 325 through 336 removed outlier: 3.763A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 341 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1121 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3027 1.33 - 1.45: 4661 1.45 - 1.57: 10554 1.57 - 1.69: 0 1.69 - 1.82: 105 Bond restraints: 18347 Sorted by residual: bond pdb=" CA PHE B 109 " pdb=" C PHE B 109 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.00e-02 1.00e+04 9.12e-01 bond pdb=" CA PHE F 109 " pdb=" C PHE F 109 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.00e-02 1.00e+04 8.35e-01 bond pdb=" CA PHE A 109 " pdb=" C PHE A 109 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.00e-02 1.00e+04 8.25e-01 bond pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.00e-02 1.00e+04 8.14e-01 bond pdb=" CA PHE G 109 " pdb=" C PHE G 109 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.00e-02 1.00e+04 7.57e-01 ... (remaining 18342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 23956 1.43 - 2.85: 780 2.85 - 4.28: 136 4.28 - 5.70: 41 5.70 - 7.13: 7 Bond angle restraints: 24920 Sorted by residual: angle pdb=" CA ILE G 296 " pdb=" CB ILE G 296 " pdb=" CG2 ILE G 296 " ideal model delta sigma weight residual 110.50 114.74 -4.24 1.70e+00 3.46e-01 6.21e+00 angle pdb=" CA ILE C 296 " pdb=" CB ILE C 296 " pdb=" CG2 ILE C 296 " ideal model delta sigma weight residual 110.50 114.69 -4.19 1.70e+00 3.46e-01 6.06e+00 angle pdb=" CA ILE E 296 " pdb=" CB ILE E 296 " pdb=" CG2 ILE E 296 " ideal model delta sigma weight residual 110.50 114.68 -4.18 1.70e+00 3.46e-01 6.05e+00 angle pdb=" CA ILE A 296 " pdb=" CB ILE A 296 " pdb=" CG2 ILE A 296 " ideal model delta sigma weight residual 110.50 114.67 -4.17 1.70e+00 3.46e-01 6.01e+00 angle pdb=" CA ILE F 296 " pdb=" CB ILE F 296 " pdb=" CG2 ILE F 296 " ideal model delta sigma weight residual 110.50 114.66 -4.16 1.70e+00 3.46e-01 5.99e+00 ... (remaining 24915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 10517 13.73 - 27.47: 830 27.47 - 41.20: 210 41.20 - 54.94: 42 54.94 - 68.67: 35 Dihedral angle restraints: 11634 sinusoidal: 5173 harmonic: 6461 Sorted by residual: dihedral pdb=" CA ARG F 299 " pdb=" C ARG F 299 " pdb=" N GLN F 300 " pdb=" CA GLN F 300 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ARG G 299 " pdb=" C ARG G 299 " pdb=" N GLN G 300 " pdb=" CA GLN G 300 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ARG C 299 " pdb=" C ARG C 299 " pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta harmonic sigma weight residual 180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 11631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1671 0.032 - 0.063: 972 0.063 - 0.095: 156 0.095 - 0.126: 113 0.126 - 0.158: 21 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CA PHE B 108 " pdb=" N PHE B 108 " pdb=" C PHE B 108 " pdb=" CB PHE B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CB ILE G 296 " pdb=" CA ILE G 296 " pdb=" CG1 ILE G 296 " pdb=" CG2 ILE G 296 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CB ILE C 296 " pdb=" CA ILE C 296 " pdb=" CG1 ILE C 296 " pdb=" CG2 ILE C 296 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 2930 not shown) Planarity restraints: 2947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 10 " 0.008 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR E 10 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 10 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 10 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 10 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR E 10 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 10 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR E 10 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 10 " 0.008 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR C 10 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 10 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C 10 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 10 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 10 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 10 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR C 10 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 10 " 0.008 2.00e-02 2.50e+03 2.43e-02 1.19e+01 pdb=" CG TYR B 10 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 10 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 10 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 10 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 10 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR B 10 " 0.036 2.00e-02 2.50e+03 ... (remaining 2944 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3774 2.79 - 3.32: 17580 3.32 - 3.84: 28549 3.84 - 4.37: 34283 4.37 - 4.90: 60823 Nonbonded interactions: 145009 Sorted by model distance: nonbonded pdb=" OH TYR A 111 " pdb=" O LEU G 52 " model vdw 2.260 3.040 nonbonded pdb=" O LEU C 52 " pdb=" OH TYR D 111 " model vdw 2.261 3.040 nonbonded pdb=" O LEU E 52 " pdb=" OH TYR F 111 " model vdw 2.264 3.040 nonbonded pdb=" O LEU F 52 " pdb=" OH TYR G 111 " model vdw 2.271 3.040 nonbonded pdb=" O LEU A 52 " pdb=" OH TYR B 111 " model vdw 2.272 3.040 ... (remaining 145004 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 1001) selection = (chain 'B' and resid 2 through 1001) selection = (chain 'C' and resid 2 through 1001) selection = (chain 'D' and resid 2 through 1001) selection = (chain 'E' and resid 2 through 1001) selection = (chain 'F' and resid 2 through 1001) selection = chain 'G' } 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: 4.410 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: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.800 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 : 0.003 0.033 18361 Z= 0.133 Angle : 0.655 7.125 24948 Z= 0.376 Chirality : 0.041 0.158 2933 Planarity : 0.006 0.065 2947 Dihedral : 11.310 68.674 7378 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2114 helix: 0.80 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -0.19 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG E 29 TYR 0.037 0.006 TYR A 10 PHE 0.015 0.002 PHE D 15 TRP 0.037 0.003 TRP F 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00279 (18347) covalent geometry : angle 0.65349 (24920) SS BOND : bond 0.00115 ( 14) SS BOND : angle 1.59452 ( 28) hydrogen bonds : bond 0.18633 ( 1121) hydrogen bonds : angle 6.51799 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8567 (mt-10) REVERT: A 91 LYS cc_start: 0.8754 (mttt) cc_final: 0.7979 (tptt) REVERT: A 197 GLN cc_start: 0.8948 (mt0) cc_final: 0.8690 (mp10) REVERT: A 316 VAL cc_start: 0.9151 (m) cc_final: 0.8950 (t) REVERT: A 325 ASN cc_start: 0.7823 (m110) cc_final: 0.7617 (p0) REVERT: A 335 GLU cc_start: 0.9018 (tt0) cc_final: 0.8451 (tp30) REVERT: B 31 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 91 LYS cc_start: 0.8785 (mttt) cc_final: 0.8085 (tptt) REVERT: B 316 VAL cc_start: 0.9108 (m) cc_final: 0.8907 (t) REVERT: B 325 ASN cc_start: 0.7749 (m110) cc_final: 0.7500 (p0) REVERT: C 31 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8545 (mt-10) REVERT: C 37 MET cc_start: 0.8883 (tpt) cc_final: 0.8680 (tpp) REVERT: C 56 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8532 (mm110) REVERT: C 91 LYS cc_start: 0.8745 (mttt) cc_final: 0.8029 (tptt) REVERT: C 316 VAL cc_start: 0.9094 (m) cc_final: 0.8880 (t) REVERT: D 31 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8526 (mt-10) REVERT: D 37 MET cc_start: 0.8848 (tpt) cc_final: 0.8570 (tpp) REVERT: D 91 LYS cc_start: 0.8766 (mttt) cc_final: 0.8035 (tptt) REVERT: D 197 GLN cc_start: 0.8952 (mt0) cc_final: 0.8692 (mp10) REVERT: D 316 VAL cc_start: 0.9101 (m) cc_final: 0.8883 (t) REVERT: E 31 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8520 (mt-10) REVERT: E 37 MET cc_start: 0.8858 (tpt) cc_final: 0.8539 (tpp) REVERT: E 91 LYS cc_start: 0.8811 (mttt) cc_final: 0.8048 (tptt) REVERT: E 325 ASN cc_start: 0.7795 (m110) cc_final: 0.7571 (p0) REVERT: F 31 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8543 (mt-10) REVERT: F 56 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8562 (mm110) REVERT: F 91 LYS cc_start: 0.8801 (mttt) cc_final: 0.8090 (tptt) REVERT: F 197 GLN cc_start: 0.8944 (mt0) cc_final: 0.8739 (mp10) REVERT: F 316 VAL cc_start: 0.9082 (m) cc_final: 0.8879 (t) REVERT: F 335 GLU cc_start: 0.9027 (tt0) cc_final: 0.8463 (tp30) REVERT: G 91 LYS cc_start: 0.8768 (mttt) cc_final: 0.8024 (tptt) REVERT: G 335 GLU cc_start: 0.9036 (tt0) cc_final: 0.8765 (tp30) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.7032 time to fit residues: 209.6028 Evaluate side-chains 196 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 100 ASN B 89 GLN B 90 GLN B 100 ASN C 89 GLN C 90 GLN C 100 ASN C 279 ASN D 89 GLN D 90 GLN D 100 ASN D 279 ASN E 90 GLN E 100 ASN F 89 GLN F 90 GLN F 100 ASN F 279 ASN G 89 GLN G 90 GLN G 100 ASN G 279 ASN G 352 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.065135 restraints weight = 29408.974| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.38 r_work: 0.2617 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18361 Z= 0.143 Angle : 0.590 7.468 24948 Z= 0.299 Chirality : 0.038 0.141 2933 Planarity : 0.004 0.026 2947 Dihedral : 6.811 51.198 3297 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.61 % Allowed : 4.61 % Favored : 94.78 % 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: 2.82 (0.19), residues: 2114 helix: 2.61 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : 0.14 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.014 0.001 TYR E 324 PHE 0.012 0.001 PHE E 109 TRP 0.021 0.002 TRP E 104 HIS 0.004 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00296 (18347) covalent geometry : angle 0.58988 (24920) SS BOND : bond 0.00102 ( 14) SS BOND : angle 0.99189 ( 28) hydrogen bonds : bond 0.05482 ( 1121) hydrogen bonds : angle 4.18238 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 91 LYS cc_start: 0.8459 (mttt) cc_final: 0.7653 (tptt) REVERT: A 197 GLN cc_start: 0.8750 (mt0) cc_final: 0.8533 (mp10) REVERT: A 325 ASN cc_start: 0.8015 (m110) cc_final: 0.7423 (p0) REVERT: A 335 GLU cc_start: 0.8938 (tt0) cc_final: 0.8539 (tp30) REVERT: B 31 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8463 (mt-10) REVERT: B 91 LYS cc_start: 0.8527 (mttt) cc_final: 0.7698 (tptt) REVERT: B 95 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6716 (mm110) REVERT: B 197 GLN cc_start: 0.8558 (mp10) cc_final: 0.7994 (mp10) REVERT: B 325 ASN cc_start: 0.7977 (m110) cc_final: 0.7473 (p0) REVERT: C 31 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 56 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8525 (mm110) REVERT: C 91 LYS cc_start: 0.8495 (mttt) cc_final: 0.7664 (tptt) REVERT: C 95 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6788 (mm110) REVERT: D 91 LYS cc_start: 0.8483 (mttt) cc_final: 0.7674 (tptt) REVERT: D 128 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8351 (mtt180) REVERT: E 31 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8459 (mt-10) REVERT: E 91 LYS cc_start: 0.8511 (mttt) cc_final: 0.7676 (tptt) REVERT: E 197 GLN cc_start: 0.8497 (mp10) cc_final: 0.8049 (mp10) REVERT: E 325 ASN cc_start: 0.7962 (m110) cc_final: 0.7415 (p0) REVERT: E 335 GLU cc_start: 0.8899 (tt0) cc_final: 0.8437 (tp30) REVERT: E 352 ASN cc_start: 0.9228 (m-40) cc_final: 0.9008 (m-40) REVERT: F 31 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8362 (mt-10) REVERT: F 56 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8511 (mm110) REVERT: F 91 LYS cc_start: 0.8545 (mttt) cc_final: 0.7732 (tptt) REVERT: F 318 HIS cc_start: 0.8832 (m90) cc_final: 0.8423 (m-70) REVERT: F 320 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8209 (ptpp) REVERT: F 335 GLU cc_start: 0.8954 (tt0) cc_final: 0.8617 (mt-10) REVERT: G 91 LYS cc_start: 0.8533 (mttt) cc_final: 0.7689 (tptt) REVERT: G 95 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6904 (mm110) REVERT: G 197 GLN cc_start: 0.8535 (mp10) cc_final: 0.8145 (mp10) REVERT: G 318 HIS cc_start: 0.8848 (m90) cc_final: 0.8560 (m-70) REVERT: G 320 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8127 (ptpp) REVERT: G 335 GLU cc_start: 0.8970 (tt0) cc_final: 0.8755 (tp30) outliers start: 12 outliers final: 2 residues processed: 220 average time/residue: 0.8254 time to fit residues: 196.9828 Evaluate side-chains 185 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 200 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 100 ASN A 279 ASN A 331 ASN B 100 ASN B 279 ASN B 331 ASN B 352 ASN C 331 ASN D 100 ASN D 331 ASN D 352 ASN E 100 ASN E 331 ASN F 100 ASN F 331 ASN G 100 ASN G 352 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.065342 restraints weight = 29697.237| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.42 r_work: 0.2632 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18361 Z= 0.125 Angle : 0.554 7.549 24948 Z= 0.272 Chirality : 0.036 0.137 2933 Planarity : 0.003 0.028 2947 Dihedral : 6.874 56.150 3297 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.41 % Allowed : 5.99 % Favored : 93.60 % 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: 2.91 (0.19), residues: 2114 helix: 2.72 (0.14), residues: 1470 sheet: -1.14 (0.59), residues: 70 loop : 0.26 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 216 TYR 0.015 0.001 TYR D 229 PHE 0.012 0.001 PHE F 12 TRP 0.017 0.002 TRP C 104 HIS 0.003 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (18347) covalent geometry : angle 0.55328 (24920) SS BOND : bond 0.00121 ( 14) SS BOND : angle 0.97557 ( 28) hydrogen bonds : bond 0.04992 ( 1121) hydrogen bonds : angle 3.91504 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8360 (mttt) cc_final: 0.7573 (tptt) REVERT: A 95 GLN cc_start: 0.7072 (mm110) cc_final: 0.6801 (mm-40) REVERT: A 197 GLN cc_start: 0.8765 (mt0) cc_final: 0.8551 (mp10) REVERT: A 325 ASN cc_start: 0.8132 (m110) cc_final: 0.7562 (p0) REVERT: B 31 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 91 LYS cc_start: 0.8274 (mttt) cc_final: 0.7495 (tptt) REVERT: B 95 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6797 (mm110) REVERT: B 143 MET cc_start: 0.8589 (mtm) cc_final: 0.8355 (mtm) REVERT: B 197 GLN cc_start: 0.8598 (mp10) cc_final: 0.8072 (mp10) REVERT: B 325 ASN cc_start: 0.8088 (m110) cc_final: 0.7610 (p0) REVERT: C 31 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 56 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8567 (mm110) REVERT: C 91 LYS cc_start: 0.8344 (mttt) cc_final: 0.7508 (tptt) REVERT: C 197 GLN cc_start: 0.8445 (mp10) cc_final: 0.8111 (mp10) REVERT: C 320 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8302 (pmtt) REVERT: C 335 GLU cc_start: 0.8854 (tt0) cc_final: 0.8383 (mt-10) REVERT: D 91 LYS cc_start: 0.8391 (mttt) cc_final: 0.7579 (tptt) REVERT: D 128 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8306 (mtt180) REVERT: D 197 GLN cc_start: 0.8462 (mp10) cc_final: 0.8149 (mp10) REVERT: D 320 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8243 (pmtt) REVERT: E 31 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8447 (mt-10) REVERT: E 37 MET cc_start: 0.8576 (tpt) cc_final: 0.8360 (tpp) REVERT: E 91 LYS cc_start: 0.8377 (mttt) cc_final: 0.7524 (tptt) REVERT: E 197 GLN cc_start: 0.8571 (mt0) cc_final: 0.8122 (mp10) REVERT: E 325 ASN cc_start: 0.8122 (m110) cc_final: 0.7603 (p0) REVERT: E 352 ASN cc_start: 0.9239 (m-40) cc_final: 0.9008 (m-40) REVERT: F 56 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8582 (mm110) REVERT: F 91 LYS cc_start: 0.8401 (mttt) cc_final: 0.7570 (tptt) REVERT: F 95 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6769 (mm110) REVERT: F 197 GLN cc_start: 0.8471 (mp10) cc_final: 0.8190 (mp10) REVERT: F 320 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8218 (pmtt) REVERT: F 335 GLU cc_start: 0.8947 (tt0) cc_final: 0.8626 (mt-10) REVERT: G 91 LYS cc_start: 0.8389 (mttt) cc_final: 0.7577 (tptt) REVERT: G 197 GLN cc_start: 0.8600 (mp10) cc_final: 0.8230 (mp10) REVERT: G 318 HIS cc_start: 0.8886 (m90) cc_final: 0.8607 (m-70) REVERT: G 320 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8347 (ptpp) REVERT: G 335 GLU cc_start: 0.8956 (tt0) cc_final: 0.8647 (mt-10) outliers start: 8 outliers final: 2 residues processed: 202 average time/residue: 0.7473 time to fit residues: 165.2372 Evaluate side-chains 196 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 120 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN B 100 ASN B 331 ASN B 352 ASN C 100 ASN C 352 ASN D 331 ASN D 352 ASN E 95 GLN E 100 ASN F 100 ASN F 331 ASN G 100 ASN G 331 ASN G 352 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.069284 restraints weight = 30041.962| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.37 r_work: 0.2727 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18361 Z= 0.115 Angle : 0.526 7.495 24948 Z= 0.255 Chirality : 0.036 0.137 2933 Planarity : 0.003 0.025 2947 Dihedral : 6.665 52.252 3297 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.51 % Allowed : 6.45 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.19), residues: 2114 helix: 2.78 (0.14), residues: 1477 sheet: -0.81 (0.60), residues: 70 loop : 0.32 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 216 TYR 0.015 0.001 TYR D 229 PHE 0.011 0.001 PHE F 12 TRP 0.013 0.002 TRP D 104 HIS 0.003 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (18347) covalent geometry : angle 0.52525 (24920) SS BOND : bond 0.00138 ( 14) SS BOND : angle 0.88282 ( 28) hydrogen bonds : bond 0.04419 ( 1121) hydrogen bonds : angle 3.75496 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8241 (mttt) cc_final: 0.7531 (tptt) REVERT: A 197 GLN cc_start: 0.8840 (mt0) cc_final: 0.8628 (mp10) REVERT: A 320 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (pmtt) REVERT: A 325 ASN cc_start: 0.8272 (m110) cc_final: 0.7854 (p0) REVERT: A 335 GLU cc_start: 0.8905 (tt0) cc_final: 0.8437 (mt-10) REVERT: B 91 LYS cc_start: 0.8194 (mttt) cc_final: 0.7496 (tptt) REVERT: B 197 GLN cc_start: 0.8686 (mp10) cc_final: 0.8168 (mp10) REVERT: B 210 MET cc_start: 0.8361 (tpp) cc_final: 0.8080 (mmt) REVERT: B 320 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8383 (pmtt) REVERT: B 325 ASN cc_start: 0.8232 (m110) cc_final: 0.7911 (p0) REVERT: B 335 GLU cc_start: 0.8872 (tt0) cc_final: 0.8424 (mt-10) REVERT: C 56 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8670 (mm110) REVERT: C 91 LYS cc_start: 0.8214 (mttt) cc_final: 0.7429 (tptt) REVERT: C 95 GLN cc_start: 0.7276 (mm110) cc_final: 0.6871 (mm110) REVERT: C 197 GLN cc_start: 0.8492 (mp10) cc_final: 0.8110 (mp10) REVERT: C 320 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8593 (pmtt) REVERT: C 335 GLU cc_start: 0.8904 (tt0) cc_final: 0.8448 (mt-10) REVERT: D 91 LYS cc_start: 0.8255 (mttt) cc_final: 0.7517 (tptt) REVERT: D 95 GLN cc_start: 0.7284 (mm110) cc_final: 0.6861 (mm-40) REVERT: D 128 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8390 (mtt180) REVERT: D 197 GLN cc_start: 0.8465 (mp10) cc_final: 0.8076 (mp10) REVERT: D 320 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (pmtt) REVERT: D 335 GLU cc_start: 0.8904 (tt0) cc_final: 0.8488 (mt-10) REVERT: E 37 MET cc_start: 0.8764 (tpt) cc_final: 0.8552 (tpp) REVERT: E 91 LYS cc_start: 0.8189 (mttt) cc_final: 0.7421 (tptt) REVERT: E 197 GLN cc_start: 0.8671 (mt0) cc_final: 0.8238 (mp10) REVERT: E 320 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8499 (pmtt) REVERT: E 325 ASN cc_start: 0.8248 (m110) cc_final: 0.7860 (p0) REVERT: E 352 ASN cc_start: 0.9265 (m-40) cc_final: 0.9029 (m-40) REVERT: F 56 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8699 (mm110) REVERT: F 91 LYS cc_start: 0.8297 (mttt) cc_final: 0.7507 (tptt) REVERT: F 95 GLN cc_start: 0.7251 (mm-40) cc_final: 0.7038 (mm110) REVERT: F 197 GLN cc_start: 0.8523 (mp10) cc_final: 0.8121 (mp10) REVERT: F 210 MET cc_start: 0.8373 (tpp) cc_final: 0.8103 (mmt) REVERT: F 320 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8367 (pmtt) REVERT: F 335 GLU cc_start: 0.8980 (tt0) cc_final: 0.8682 (mt-10) REVERT: G 91 LYS cc_start: 0.8266 (mttt) cc_final: 0.7532 (tptt) REVERT: G 95 GLN cc_start: 0.7329 (mm110) cc_final: 0.7046 (mm-40) REVERT: G 197 GLN cc_start: 0.8670 (mp10) cc_final: 0.8315 (mp10) REVERT: G 210 MET cc_start: 0.8391 (tpp) cc_final: 0.8137 (mmt) REVERT: G 320 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8330 (pmtt) REVERT: G 335 GLU cc_start: 0.8957 (tt0) cc_final: 0.8675 (mt-10) outliers start: 10 outliers final: 3 residues processed: 197 average time/residue: 0.7819 time to fit residues: 168.3287 Evaluate side-chains 189 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 99 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 352 ASN B 100 ASN B 331 ASN B 352 ASN C 331 ASN D 352 ASN E 100 ASN E 331 ASN F 100 ASN F 352 ASN G 352 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.069040 restraints weight = 29804.767| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.37 r_work: 0.2725 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18361 Z= 0.113 Angle : 0.515 7.527 24948 Z= 0.248 Chirality : 0.036 0.136 2933 Planarity : 0.003 0.025 2947 Dihedral : 6.597 55.557 3297 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.77 % Allowed : 6.71 % Favored : 92.52 % 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: 3.15 (0.19), residues: 2114 helix: 2.89 (0.14), residues: 1477 sheet: -0.77 (0.60), residues: 70 loop : 0.29 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 216 TYR 0.015 0.001 TYR D 229 PHE 0.010 0.001 PHE F 12 TRP 0.012 0.001 TRP G 104 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00242 (18347) covalent geometry : angle 0.51472 (24920) SS BOND : bond 0.00108 ( 14) SS BOND : angle 0.81356 ( 28) hydrogen bonds : bond 0.04318 ( 1121) hydrogen bonds : angle 3.68504 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8163 (mttt) cc_final: 0.7430 (tptt) REVERT: A 95 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6822 (mm110) REVERT: A 197 GLN cc_start: 0.8841 (mt0) cc_final: 0.8640 (mp10) REVERT: A 210 MET cc_start: 0.8364 (tpp) cc_final: 0.8109 (mmt) REVERT: A 320 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8462 (pmtt) REVERT: A 325 ASN cc_start: 0.8349 (m110) cc_final: 0.7953 (p0) REVERT: A 335 GLU cc_start: 0.8916 (tt0) cc_final: 0.8446 (mt-10) REVERT: B 91 LYS cc_start: 0.8147 (mttt) cc_final: 0.7369 (tptt) REVERT: B 95 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6963 (mm110) REVERT: B 197 GLN cc_start: 0.8701 (mp10) cc_final: 0.8207 (mp10) REVERT: B 210 MET cc_start: 0.8337 (tpp) cc_final: 0.8059 (mmt) REVERT: B 320 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8472 (pmtt) REVERT: B 325 ASN cc_start: 0.8238 (m110) cc_final: 0.7909 (p0) REVERT: B 335 GLU cc_start: 0.8873 (tt0) cc_final: 0.8422 (mt-10) REVERT: C 91 LYS cc_start: 0.8140 (mttt) cc_final: 0.7372 (tptt) REVERT: C 95 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6923 (mm110) REVERT: C 197 GLN cc_start: 0.8544 (mp10) cc_final: 0.8106 (mp10) REVERT: C 210 MET cc_start: 0.8366 (tpp) cc_final: 0.8127 (mmt) REVERT: C 320 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8453 (pmtt) REVERT: C 335 GLU cc_start: 0.8900 (tt0) cc_final: 0.8431 (mt-10) REVERT: D 91 LYS cc_start: 0.8155 (mttt) cc_final: 0.7383 (tptt) REVERT: D 95 GLN cc_start: 0.7373 (mm110) cc_final: 0.7122 (mm-40) REVERT: D 197 GLN cc_start: 0.8501 (mp10) cc_final: 0.8082 (mp10) REVERT: D 210 MET cc_start: 0.8327 (tpp) cc_final: 0.8072 (mmm) REVERT: D 320 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8595 (pmtt) REVERT: D 335 GLU cc_start: 0.8909 (tt0) cc_final: 0.8483 (mt-10) REVERT: E 91 LYS cc_start: 0.8096 (mttt) cc_final: 0.7377 (tptt) REVERT: E 197 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: E 210 MET cc_start: 0.8547 (tpp) cc_final: 0.8298 (mmm) REVERT: E 320 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8490 (pmtt) REVERT: E 325 ASN cc_start: 0.8301 (m110) cc_final: 0.7917 (p0) REVERT: E 335 GLU cc_start: 0.8927 (tt0) cc_final: 0.8464 (mt-10) REVERT: E 352 ASN cc_start: 0.9269 (m-40) cc_final: 0.9044 (m-40) REVERT: F 91 LYS cc_start: 0.8197 (mttt) cc_final: 0.7431 (tptt) REVERT: F 95 GLN cc_start: 0.7348 (mm-40) cc_final: 0.7123 (mm110) REVERT: F 197 GLN cc_start: 0.8566 (mp10) cc_final: 0.8091 (mp10) REVERT: F 320 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8556 (pmtt) REVERT: F 335 GLU cc_start: 0.8979 (tt0) cc_final: 0.8682 (mt-10) REVERT: G 91 LYS cc_start: 0.8187 (mttt) cc_final: 0.7474 (tptt) REVERT: G 197 GLN cc_start: 0.8663 (mp10) cc_final: 0.8310 (mp10) REVERT: G 210 MET cc_start: 0.8365 (tpp) cc_final: 0.8131 (mmt) REVERT: G 320 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8433 (pmtt) REVERT: G 335 GLU cc_start: 0.8972 (tt0) cc_final: 0.8697 (mt-10) outliers start: 15 outliers final: 3 residues processed: 209 average time/residue: 0.7129 time to fit residues: 163.4436 Evaluate side-chains 201 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 chunk 142 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 352 ASN B 331 ASN B 352 ASN C 56 GLN C 331 ASN D 100 ASN D 134 HIS D 352 ASN E 100 ASN E 331 ASN F 352 ASN G 95 GLN G 331 ASN G 352 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.066689 restraints weight = 29603.796| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.38 r_work: 0.2684 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18361 Z= 0.127 Angle : 0.524 7.670 24948 Z= 0.252 Chirality : 0.036 0.135 2933 Planarity : 0.003 0.024 2947 Dihedral : 6.592 50.816 3297 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.92 % Allowed : 7.01 % Favored : 92.06 % 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: 3.14 (0.19), residues: 2114 helix: 2.90 (0.14), residues: 1477 sheet: -0.72 (0.60), residues: 70 loop : 0.23 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 128 TYR 0.015 0.001 TYR D 229 PHE 0.010 0.001 PHE B 243 TRP 0.012 0.002 TRP A 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00289 (18347) covalent geometry : angle 0.52398 (24920) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.74016 ( 28) hydrogen bonds : bond 0.04459 ( 1121) hydrogen bonds : angle 3.68552 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8174 (mttt) cc_final: 0.7414 (tptt) REVERT: A 197 GLN cc_start: 0.8809 (mt0) cc_final: 0.8587 (mp10) REVERT: A 210 MET cc_start: 0.8336 (tpp) cc_final: 0.8108 (mmt) REVERT: A 320 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8486 (pmtt) REVERT: A 325 ASN cc_start: 0.8338 (m110) cc_final: 0.7932 (p0) REVERT: A 335 GLU cc_start: 0.8901 (tt0) cc_final: 0.8434 (mt-10) REVERT: A 342 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7656 (tmtt) REVERT: B 91 LYS cc_start: 0.8117 (mttt) cc_final: 0.7308 (tptt) REVERT: B 95 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6850 (mm110) REVERT: B 197 GLN cc_start: 0.8658 (mp10) cc_final: 0.8155 (mp10) REVERT: B 210 MET cc_start: 0.8277 (tpp) cc_final: 0.8062 (mmm) REVERT: B 320 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8410 (pmtt) REVERT: B 325 ASN cc_start: 0.8290 (m110) cc_final: 0.7899 (p0) REVERT: B 335 GLU cc_start: 0.8844 (tt0) cc_final: 0.8380 (mt-10) REVERT: C 91 LYS cc_start: 0.8136 (mttt) cc_final: 0.7352 (tptt) REVERT: C 95 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6688 (mm110) REVERT: C 197 GLN cc_start: 0.8505 (mp10) cc_final: 0.8027 (mp10) REVERT: C 210 MET cc_start: 0.8307 (tpp) cc_final: 0.8061 (mmt) REVERT: C 320 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (pmtt) REVERT: C 335 GLU cc_start: 0.8877 (tt0) cc_final: 0.8406 (mt-10) REVERT: D 91 LYS cc_start: 0.8122 (mttt) cc_final: 0.7364 (tptt) REVERT: D 95 GLN cc_start: 0.7337 (mm110) cc_final: 0.7043 (mm110) REVERT: D 197 GLN cc_start: 0.8489 (mp10) cc_final: 0.8045 (mp10) REVERT: D 210 MET cc_start: 0.8288 (tpp) cc_final: 0.8034 (mmt) REVERT: D 320 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8597 (pmtt) REVERT: D 335 GLU cc_start: 0.8902 (tt0) cc_final: 0.8469 (mt-10) REVERT: E 37 MET cc_start: 0.8668 (tpt) cc_final: 0.8432 (tpp) REVERT: E 91 LYS cc_start: 0.8101 (mttt) cc_final: 0.7305 (tptt) REVERT: E 197 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: E 210 MET cc_start: 0.8448 (tpp) cc_final: 0.8188 (mmm) REVERT: E 320 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8434 (pmtt) REVERT: E 325 ASN cc_start: 0.8308 (m110) cc_final: 0.7887 (p0) REVERT: E 352 ASN cc_start: 0.9268 (m-40) cc_final: 0.9043 (m-40) REVERT: F 91 LYS cc_start: 0.8171 (mttt) cc_final: 0.7372 (tptt) REVERT: F 197 GLN cc_start: 0.8538 (mp10) cc_final: 0.8075 (mp10) REVERT: F 320 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8572 (pmtt) REVERT: F 335 GLU cc_start: 0.8965 (tt0) cc_final: 0.8660 (mt-10) REVERT: G 91 LYS cc_start: 0.8138 (mttt) cc_final: 0.7382 (tptt) REVERT: G 143 MET cc_start: 0.8646 (mtm) cc_final: 0.8291 (mmm) REVERT: G 197 GLN cc_start: 0.8648 (mp10) cc_final: 0.8307 (mp10) REVERT: G 320 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8404 (pmtt) REVERT: G 335 GLU cc_start: 0.8955 (tt0) cc_final: 0.8679 (mt-10) outliers start: 18 outliers final: 4 residues processed: 203 average time/residue: 0.7583 time to fit residues: 168.2088 Evaluate side-chains 206 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 177 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 185 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 352 ASN B 100 ASN B 331 ASN B 352 ASN C 100 ASN C 134 HIS C 204 ASN D 134 HIS D 352 ASN E 331 ASN F 352 ASN G 318 HIS G 331 ASN G 352 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.064903 restraints weight = 29809.793| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.38 r_work: 0.2652 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18361 Z= 0.148 Angle : 0.542 7.957 24948 Z= 0.260 Chirality : 0.037 0.135 2933 Planarity : 0.003 0.024 2947 Dihedral : 6.707 45.069 3297 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.08 % Allowed : 7.58 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.09 (0.19), residues: 2114 helix: 2.89 (0.14), residues: 1477 sheet: -0.80 (0.60), residues: 70 loop : 0.10 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 29 TYR 0.014 0.001 TYR D 229 PHE 0.017 0.001 PHE E 295 TRP 0.013 0.002 TRP A 104 HIS 0.002 0.000 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00344 (18347) covalent geometry : angle 0.54192 (24920) SS BOND : bond 0.00191 ( 14) SS BOND : angle 0.69249 ( 28) hydrogen bonds : bond 0.04752 ( 1121) hydrogen bonds : angle 3.75060 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8208 (mttt) cc_final: 0.7427 (tptt) REVERT: A 95 GLN cc_start: 0.7188 (mm110) cc_final: 0.6937 (mm110) REVERT: A 197 GLN cc_start: 0.8806 (mt0) cc_final: 0.8590 (mp10) REVERT: A 210 MET cc_start: 0.8342 (tpp) cc_final: 0.8105 (mmt) REVERT: A 320 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8543 (pmtt) REVERT: A 325 ASN cc_start: 0.8383 (m110) cc_final: 0.7922 (p0) REVERT: A 335 GLU cc_start: 0.8926 (tt0) cc_final: 0.8467 (mt-10) REVERT: B 91 LYS cc_start: 0.8162 (mttt) cc_final: 0.7377 (tptt) REVERT: B 95 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6864 (mm110) REVERT: B 197 GLN cc_start: 0.8659 (mp10) cc_final: 0.8174 (mp10) REVERT: B 210 MET cc_start: 0.8307 (tpp) cc_final: 0.8093 (mmt) REVERT: B 320 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8466 (pmtt) REVERT: B 325 ASN cc_start: 0.8347 (m110) cc_final: 0.7908 (p0) REVERT: B 335 GLU cc_start: 0.8847 (tt0) cc_final: 0.8396 (mt-10) REVERT: C 91 LYS cc_start: 0.8159 (mttt) cc_final: 0.7377 (tptt) REVERT: C 95 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6807 (mm110) REVERT: C 197 GLN cc_start: 0.8516 (mp10) cc_final: 0.8054 (mp10) REVERT: C 210 MET cc_start: 0.8329 (tpp) cc_final: 0.8119 (mmt) REVERT: C 320 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8629 (pmtt) REVERT: C 335 GLU cc_start: 0.8891 (tt0) cc_final: 0.8444 (mt-10) REVERT: D 91 LYS cc_start: 0.8137 (mttt) cc_final: 0.7379 (tptt) REVERT: D 95 GLN cc_start: 0.7409 (mm110) cc_final: 0.7116 (mm-40) REVERT: D 197 GLN cc_start: 0.8513 (mp10) cc_final: 0.8074 (mp10) REVERT: D 210 MET cc_start: 0.8328 (tpp) cc_final: 0.8043 (mmm) REVERT: D 320 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8626 (pmtt) REVERT: D 335 GLU cc_start: 0.8904 (tt0) cc_final: 0.8473 (mt-10) REVERT: D 342 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7807 (tmmt) REVERT: E 91 LYS cc_start: 0.8130 (mttt) cc_final: 0.7312 (tptt) REVERT: E 197 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: E 210 MET cc_start: 0.8474 (tpp) cc_final: 0.8249 (mmt) REVERT: E 320 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8461 (pmtt) REVERT: E 325 ASN cc_start: 0.8357 (m110) cc_final: 0.7904 (p0) REVERT: E 352 ASN cc_start: 0.9273 (m-40) cc_final: 0.9060 (m-40) REVERT: F 91 LYS cc_start: 0.8190 (mttt) cc_final: 0.7381 (tptt) REVERT: F 197 GLN cc_start: 0.8539 (mp10) cc_final: 0.8035 (mp10) REVERT: F 320 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8590 (pmtt) REVERT: F 335 GLU cc_start: 0.8986 (tt0) cc_final: 0.8678 (mt-10) REVERT: G 91 LYS cc_start: 0.8189 (mttt) cc_final: 0.7420 (tptt) REVERT: G 143 MET cc_start: 0.8652 (mtm) cc_final: 0.8314 (mmm) REVERT: G 197 GLN cc_start: 0.8641 (mp10) cc_final: 0.8291 (mp10) REVERT: G 320 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8423 (pmtt) REVERT: G 335 GLU cc_start: 0.8968 (tt0) cc_final: 0.8696 (mt-10) outliers start: 21 outliers final: 2 residues processed: 211 average time/residue: 0.7639 time to fit residues: 176.1485 Evaluate side-chains 205 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 55 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 105 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 352 ASN B 100 ASN B 331 ASN B 352 ASN C 100 ASN C 134 HIS C 204 ASN D 134 HIS D 352 ASN E 134 HIS E 331 ASN F 100 ASN F 352 ASN G 318 HIS G 352 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.066782 restraints weight = 29684.340| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.36 r_work: 0.2678 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18361 Z= 0.123 Angle : 0.546 10.519 24948 Z= 0.259 Chirality : 0.036 0.134 2933 Planarity : 0.003 0.024 2947 Dihedral : 6.620 44.188 3297 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.92 % Allowed : 8.09 % Favored : 90.99 % 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: 3.06 (0.19), residues: 2114 helix: 2.90 (0.14), residues: 1477 sheet: -0.80 (0.60), residues: 70 loop : -0.02 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 128 TYR 0.014 0.001 TYR B 229 PHE 0.009 0.001 PHE A 243 TRP 0.015 0.002 TRP A 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00276 (18347) covalent geometry : angle 0.54575 (24920) SS BOND : bond 0.00152 ( 14) SS BOND : angle 0.72197 ( 28) hydrogen bonds : bond 0.04411 ( 1121) hydrogen bonds : angle 3.67691 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8155 (mttt) cc_final: 0.7390 (tptt) REVERT: A 95 GLN cc_start: 0.7216 (mm110) cc_final: 0.6942 (mm110) REVERT: A 197 GLN cc_start: 0.8804 (mt0) cc_final: 0.8570 (mp10) REVERT: A 210 MET cc_start: 0.8345 (tpp) cc_final: 0.8101 (mmt) REVERT: A 320 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8582 (pmtt) REVERT: A 325 ASN cc_start: 0.8384 (m110) cc_final: 0.7950 (p0) REVERT: A 335 GLU cc_start: 0.8905 (tt0) cc_final: 0.8442 (mt-10) REVERT: B 91 LYS cc_start: 0.8101 (mttt) cc_final: 0.7324 (tptt) REVERT: B 95 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6814 (mm-40) REVERT: B 197 GLN cc_start: 0.8649 (mp10) cc_final: 0.8149 (mp10) REVERT: B 320 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8514 (pmtt) REVERT: B 325 ASN cc_start: 0.8354 (m110) cc_final: 0.7908 (p0) REVERT: B 335 GLU cc_start: 0.8840 (tt0) cc_final: 0.8377 (mt-10) REVERT: C 91 LYS cc_start: 0.8105 (mttt) cc_final: 0.7314 (tptt) REVERT: C 95 GLN cc_start: 0.7316 (mm110) cc_final: 0.6804 (mm110) REVERT: C 197 GLN cc_start: 0.8502 (mp10) cc_final: 0.8033 (mp10) REVERT: C 210 MET cc_start: 0.8306 (tpp) cc_final: 0.8089 (mmt) REVERT: C 320 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8652 (pmtt) REVERT: C 335 GLU cc_start: 0.8880 (tt0) cc_final: 0.8430 (mt-10) REVERT: D 91 LYS cc_start: 0.8097 (mttt) cc_final: 0.7363 (tptt) REVERT: D 197 GLN cc_start: 0.8507 (mp10) cc_final: 0.8053 (mp10) REVERT: D 210 MET cc_start: 0.8316 (tpp) cc_final: 0.8026 (mmm) REVERT: D 320 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8661 (pmtt) REVERT: D 335 GLU cc_start: 0.8902 (tt0) cc_final: 0.8493 (mt-10) REVERT: E 91 LYS cc_start: 0.8069 (mttt) cc_final: 0.7258 (tptt) REVERT: E 197 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: E 210 MET cc_start: 0.8455 (tpp) cc_final: 0.8180 (mmm) REVERT: E 320 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8532 (pmtt) REVERT: E 325 ASN cc_start: 0.8369 (m110) cc_final: 0.7866 (p0) REVERT: F 91 LYS cc_start: 0.8085 (mttt) cc_final: 0.7265 (tptt) REVERT: F 197 GLN cc_start: 0.8526 (mp10) cc_final: 0.8024 (mp10) REVERT: F 320 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8596 (pmtt) REVERT: F 335 GLU cc_start: 0.8974 (tt0) cc_final: 0.8663 (mt-10) REVERT: G 91 LYS cc_start: 0.8108 (mttt) cc_final: 0.7343 (tptt) REVERT: G 97 GLU cc_start: 0.7269 (pp20) cc_final: 0.7047 (pm20) REVERT: G 143 MET cc_start: 0.8636 (mtm) cc_final: 0.8317 (mmm) REVERT: G 197 GLN cc_start: 0.8630 (mp10) cc_final: 0.8279 (mp10) REVERT: G 320 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8516 (pmtt) REVERT: G 335 GLU cc_start: 0.8957 (tt0) cc_final: 0.8683 (mt-10) outliers start: 18 outliers final: 2 residues processed: 204 average time/residue: 0.7526 time to fit residues: 168.1584 Evaluate side-chains 201 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 215 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 179 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 352 ASN B 100 ASN B 204 ASN B 331 ASN B 352 ASN C 100 ASN C 134 HIS C 204 ASN C 352 ASN D 95 GLN D 134 HIS D 352 ASN E 134 HIS E 352 ASN F 352 ASN G 318 HIS G 331 ASN G 352 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.066510 restraints weight = 29621.034| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.34 r_work: 0.2670 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18361 Z= 0.131 Angle : 0.546 10.219 24948 Z= 0.259 Chirality : 0.036 0.134 2933 Planarity : 0.003 0.049 2947 Dihedral : 6.628 43.008 3297 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.13 % Allowed : 8.40 % Favored : 90.48 % 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: 3.05 (0.19), residues: 2114 helix: 2.92 (0.14), residues: 1477 sheet: -0.74 (0.59), residues: 70 loop : -0.10 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 152 TYR 0.014 0.001 TYR A 324 PHE 0.014 0.001 PHE E 295 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (18347) covalent geometry : angle 0.54626 (24920) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.67994 ( 28) hydrogen bonds : bond 0.04493 ( 1121) hydrogen bonds : angle 3.68711 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8151 (mttt) cc_final: 0.7372 (tptt) REVERT: A 95 GLN cc_start: 0.7272 (mm110) cc_final: 0.6967 (mm110) REVERT: A 197 GLN cc_start: 0.8804 (mt0) cc_final: 0.8568 (mp10) REVERT: A 210 MET cc_start: 0.8352 (tpp) cc_final: 0.8123 (mmt) REVERT: A 320 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (pmtt) REVERT: A 325 ASN cc_start: 0.8380 (m110) cc_final: 0.7933 (p0) REVERT: A 335 GLU cc_start: 0.8912 (tt0) cc_final: 0.8469 (mt-10) REVERT: B 91 LYS cc_start: 0.8096 (mttt) cc_final: 0.7345 (tptt) REVERT: B 197 GLN cc_start: 0.8653 (mp10) cc_final: 0.8167 (mp10) REVERT: B 320 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8526 (pmtt) REVERT: B 325 ASN cc_start: 0.8402 (m110) cc_final: 0.7826 (p0) REVERT: B 335 GLU cc_start: 0.8853 (tt0) cc_final: 0.8403 (mt-10) REVERT: C 91 LYS cc_start: 0.8097 (mttt) cc_final: 0.7315 (tptt) REVERT: C 95 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6833 (mm110) REVERT: C 197 GLN cc_start: 0.8508 (mp10) cc_final: 0.8030 (mp10) REVERT: C 320 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (pmtt) REVERT: C 335 GLU cc_start: 0.8887 (tt0) cc_final: 0.8442 (mt-10) REVERT: D 91 LYS cc_start: 0.8065 (mttt) cc_final: 0.7315 (tptt) REVERT: D 197 GLN cc_start: 0.8508 (mp10) cc_final: 0.8069 (mp10) REVERT: D 320 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8700 (pmtt) REVERT: D 335 GLU cc_start: 0.8906 (tt0) cc_final: 0.8500 (mt-10) REVERT: E 91 LYS cc_start: 0.8061 (mttt) cc_final: 0.7235 (tptt) REVERT: E 197 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8195 (mp10) REVERT: E 210 MET cc_start: 0.8465 (tpp) cc_final: 0.8235 (mmt) REVERT: E 320 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8626 (pmtt) REVERT: E 325 ASN cc_start: 0.8388 (m110) cc_final: 0.7890 (p0) REVERT: F 91 LYS cc_start: 0.8080 (mttt) cc_final: 0.7276 (tptt) REVERT: F 197 GLN cc_start: 0.8522 (mp10) cc_final: 0.8053 (mp10) REVERT: F 320 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8657 (pmtt) REVERT: F 335 GLU cc_start: 0.8981 (tt0) cc_final: 0.8680 (mt-10) REVERT: G 91 LYS cc_start: 0.8091 (mttt) cc_final: 0.7325 (tptt) REVERT: G 143 MET cc_start: 0.8636 (mtm) cc_final: 0.8281 (mmm) REVERT: G 197 GLN cc_start: 0.8619 (mp10) cc_final: 0.8267 (mp10) REVERT: G 320 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8521 (pmtt) REVERT: G 335 GLU cc_start: 0.8967 (tt0) cc_final: 0.8690 (mt-10) outliers start: 22 outliers final: 4 residues processed: 205 average time/residue: 0.7499 time to fit residues: 167.9449 Evaluate side-chains 205 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 331 ASN A 352 ASN B 100 ASN B 331 ASN B 352 ASN C 56 GLN C 100 ASN C 134 HIS C 204 ASN D 134 HIS D 352 ASN E 134 HIS E 318 HIS E 352 ASN F 100 ASN F 352 ASN G 204 ASN G 318 HIS G 352 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.063995 restraints weight = 29506.080| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.40 r_work: 0.2641 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18361 Z= 0.165 Angle : 0.583 10.654 24948 Z= 0.275 Chirality : 0.037 0.134 2933 Planarity : 0.003 0.035 2947 Dihedral : 6.737 39.581 3297 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.02 % Allowed : 8.40 % Favored : 90.58 % 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: 3.01 (0.19), residues: 2114 helix: 2.90 (0.14), residues: 1477 sheet: -0.73 (0.59), residues: 70 loop : -0.16 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 152 TYR 0.018 0.001 TYR A 324 PHE 0.012 0.001 PHE A 243 TRP 0.013 0.002 TRP A 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00393 (18347) covalent geometry : angle 0.58268 (24920) SS BOND : bond 0.00203 ( 14) SS BOND : angle 0.63983 ( 28) hydrogen bonds : bond 0.04745 ( 1121) hydrogen bonds : angle 3.73212 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8185 (mttt) cc_final: 0.7396 (tptt) REVERT: A 95 GLN cc_start: 0.7288 (mm110) cc_final: 0.6986 (mm110) REVERT: A 97 GLU cc_start: 0.7376 (pp20) cc_final: 0.7139 (pm20) REVERT: A 197 GLN cc_start: 0.8829 (mt0) cc_final: 0.8584 (mp10) REVERT: A 210 MET cc_start: 0.8365 (tpp) cc_final: 0.8125 (mmt) REVERT: A 320 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8589 (pmtt) REVERT: A 325 ASN cc_start: 0.8384 (m110) cc_final: 0.7924 (p0) REVERT: A 335 GLU cc_start: 0.8917 (tt0) cc_final: 0.8474 (mt-10) REVERT: B 91 LYS cc_start: 0.8167 (mttt) cc_final: 0.7407 (tptt) REVERT: B 197 GLN cc_start: 0.8655 (mp10) cc_final: 0.8154 (mp10) REVERT: B 320 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8538 (pmtt) REVERT: B 325 ASN cc_start: 0.8412 (m110) cc_final: 0.7838 (p0) REVERT: B 335 GLU cc_start: 0.8861 (tt0) cc_final: 0.8394 (mt-10) REVERT: C 91 LYS cc_start: 0.8147 (mttt) cc_final: 0.7342 (tptt) REVERT: C 95 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6829 (mm110) REVERT: C 197 GLN cc_start: 0.8502 (mp10) cc_final: 0.8018 (mp10) REVERT: C 320 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (pmtt) REVERT: C 335 GLU cc_start: 0.8891 (tt0) cc_final: 0.8439 (mt-10) REVERT: D 91 LYS cc_start: 0.8054 (mttt) cc_final: 0.7290 (tptt) REVERT: D 97 GLU cc_start: 0.7367 (pp20) cc_final: 0.7110 (pm20) REVERT: D 197 GLN cc_start: 0.8509 (mp10) cc_final: 0.8055 (mp10) REVERT: D 210 MET cc_start: 0.8385 (tpp) cc_final: 0.8145 (mmm) REVERT: D 320 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8688 (pmtt) REVERT: D 335 GLU cc_start: 0.8908 (tt0) cc_final: 0.8504 (mt-10) REVERT: E 91 LYS cc_start: 0.8087 (mttt) cc_final: 0.7258 (tptt) REVERT: E 97 GLU cc_start: 0.7257 (pp20) cc_final: 0.6969 (pm20) REVERT: E 197 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: E 210 MET cc_start: 0.8463 (tpp) cc_final: 0.8195 (mmm) REVERT: E 320 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8644 (pmtt) REVERT: E 325 ASN cc_start: 0.8410 (m110) cc_final: 0.7893 (p0) REVERT: F 91 LYS cc_start: 0.8103 (mttt) cc_final: 0.7304 (tptt) REVERT: F 197 GLN cc_start: 0.8528 (mp10) cc_final: 0.8013 (mp10) REVERT: F 320 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8667 (pmtt) REVERT: F 335 GLU cc_start: 0.8992 (tt0) cc_final: 0.8699 (mt-10) REVERT: G 91 LYS cc_start: 0.8142 (mttt) cc_final: 0.7375 (tptt) REVERT: G 97 GLU cc_start: 0.7263 (pp20) cc_final: 0.6911 (pm20) REVERT: G 143 MET cc_start: 0.8646 (mtm) cc_final: 0.8349 (mmm) REVERT: G 197 GLN cc_start: 0.8647 (mp10) cc_final: 0.8269 (mp10) REVERT: G 320 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8570 (pmtt) REVERT: G 335 GLU cc_start: 0.8981 (tt0) cc_final: 0.8698 (mt-10) outliers start: 20 outliers final: 4 residues processed: 204 average time/residue: 0.7334 time to fit residues: 163.2334 Evaluate side-chains 202 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 320 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 49 optimal weight: 4.9990 chunk 213 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN B 100 ASN B 204 ASN B 331 ASN B 352 ASN C 56 GLN C 134 HIS C 204 ASN D 134 HIS D 352 ASN E 134 HIS E 318 HIS E 352 ASN F 100 ASN F 204 ASN F 352 ASN G 318 HIS G 352 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.066739 restraints weight = 29685.368| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.40 r_work: 0.2700 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18361 Z= 0.112 Angle : 0.557 11.701 24948 Z= 0.262 Chirality : 0.036 0.134 2933 Planarity : 0.003 0.047 2947 Dihedral : 6.511 41.671 3297 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.97 % Allowed : 8.55 % Favored : 90.48 % 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: 3.04 (0.19), residues: 2114 helix: 2.92 (0.14), residues: 1477 sheet: -0.64 (0.59), residues: 70 loop : -0.13 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 152 TYR 0.017 0.001 TYR A 324 PHE 0.011 0.001 PHE E 295 TRP 0.017 0.002 TRP A 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00240 (18347) covalent geometry : angle 0.55699 (24920) SS BOND : bond 0.00103 ( 14) SS BOND : angle 0.70369 ( 28) hydrogen bonds : bond 0.04124 ( 1121) hydrogen bonds : angle 3.60968 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7226.22 seconds wall clock time: 123 minutes 40.06 seconds (7420.06 seconds total)