Starting phenix.real_space_refine on Sat Jul 4 11:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5l_27914/07_2026/8e5l_27914_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians P 21 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12533 2.51 5 N 3540 2.21 5 O 3832 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20058 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.13, per 1000 atoms: 0.21 Number of scatterers: 20058 At special positions: 0 Unit cell: (145.32, 126.636, 137.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 21 15.00 Mg 6 11.99 F 18 9.00 O 3832 8.00 N 3540 7.00 C 12533 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 49.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'e' and resid 2 through 9 Processing helix chain 'e' and resid 10 through 22 Processing helix chain 'e' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 132 through 136 Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 235 through 255 Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 338 removed outlier: 3.554A pdb=" N GLU e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 371 Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 391 through 404 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS e 417 " --> pdb=" O PHE e 413 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 Processing helix chain 'f' and resid 10 through 22 Processing helix chain 'f' and resid 30 through 45 removed outlier: 3.705A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 90 Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 132 through 136 Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 221 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 335 removed outlier: 3.717A pdb=" N GLU f 329 " --> pdb=" O SER f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 371 Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 391 through 404 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.718A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS f 417 " --> pdb=" O PHE f 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 Processing helix chain 'c' and resid 10 through 22 Processing helix chain 'c' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 90 Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.270A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 221 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU c 333 " --> pdb=" O GLU c 329 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 371 Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 391 through 404 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS c 417 " --> pdb=" O PHE c 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 Processing helix chain 'b' and resid 10 through 22 Processing helix chain 'b' and resid 30 through 45 removed outlier: 3.704A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 90 Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 132 through 136 Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 221 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 335 removed outlier: 3.643A pdb=" N GLU b 333 " --> pdb=" O GLU b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 391 through 404 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.722A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS b 417 " --> pdb=" O PHE b 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 10 through 22 Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.702A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 90 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 132 through 136 Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 221 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 337 removed outlier: 4.203A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 371 Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 391 through 404 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS a 417 " --> pdb=" O PHE a 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 Processing helix chain 'd' and resid 10 through 22 Processing helix chain 'd' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 90 Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.267A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 221 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 333 Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 371 Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 391 through 404 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR e 96 " --> pdb=" O VAL e 119 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL e 119 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER e 98 " --> pdb=" O ASN e 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS e 115 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG e 102 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.802A pdb=" N ASN e 306 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.476A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA e 317 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU e 342 " --> pdb=" O GLY e 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY e 364 " --> pdb=" O GLU e 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR f 96 " --> pdb=" O VAL f 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL f 119 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER f 98 " --> pdb=" O ASN f 117 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS f 115 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG f 102 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU f 113 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.805A pdb=" N ASN f 306 " --> pdb=" O LEU f 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.480A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA f 317 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU f 342 " --> pdb=" O GLY f 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY f 364 " --> pdb=" O GLU f 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR c 96 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL c 119 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER c 98 " --> pdb=" O ASN c 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS c 115 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG c 102 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN c 306 " --> pdb=" O LEU c 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.479A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA c 317 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU c 342 " --> pdb=" O GLY c 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY c 364 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR b 96 " --> pdb=" O VAL b 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 119 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 98 " --> pdb=" O ASN b 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS b 115 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG b 102 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU b 113 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN b 306 " --> pdb=" O LEU b 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA b 317 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU b 342 " --> pdb=" O GLY b 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY b 364 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'a' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR a 96 " --> pdb=" O VAL a 119 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL a 119 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER a 98 " --> pdb=" O ASN a 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS a 115 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG a 102 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN a 306 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA a 317 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU a 342 " --> pdb=" O GLY a 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY a 364 " --> pdb=" O GLU a 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR d 96 " --> pdb=" O VAL d 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL d 119 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER d 98 " --> pdb=" O ASN d 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS d 115 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG d 102 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU d 113 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.806A pdb=" N ASN d 306 " --> pdb=" O LEU d 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA d 317 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 364 " --> pdb=" O GLU d 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 944 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.23 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: 4755 1.33 - 1.45: 3619 1.45 - 1.57: 11764 1.57 - 1.69: 35 1.69 - 1.81: 198 Bond restraints: 20371 Sorted by residual: bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF f1002 " pdb="BE BEF f1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 27286 2.88 - 5.77: 167 5.77 - 8.65: 38 8.65 - 11.53: 6 11.53 - 14.41: 6 Bond angle restraints: 27503 Sorted by residual: angle pdb=" N ASP f 322 " pdb=" CA ASP f 322 " pdb=" C ASP f 322 " ideal model delta sigma weight residual 112.58 105.31 7.27 1.22e+00 6.72e-01 3.55e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.73 6.60 1.21e+00 6.83e-01 2.97e+01 angle pdb=" N GLU c 334 " pdb=" CA GLU c 334 " pdb=" C GLU c 334 " ideal model delta sigma weight residual 111.33 105.04 6.29 1.21e+00 6.83e-01 2.70e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 12396 29.81 - 59.62: 154 59.62 - 89.43: 45 89.43 - 119.24: 2 119.24 - 149.05: 10 Dihedral angle restraints: 12607 sinusoidal: 5413 harmonic: 7194 Sorted by residual: dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.05 -149.05 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP e1000 " pdb=" O3A ADP e1000 " pdb=" PB ADP e1000 " pdb=" PA ADP e1000 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.98 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PA ADP d1000 " pdb=" PB ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 84.41 -144.41 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2600 0.052 - 0.103: 412 0.103 - 0.155: 112 0.155 - 0.206: 10 0.206 - 0.258: 1 Chirality restraints: 3135 Sorted by residual: chirality pdb=" C3' A 7 1 " pdb=" C4' A 7 1 " pdb=" O3' A 7 1 " pdb=" C2' A 7 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL d 330 " pdb=" N VAL d 330 " pdb=" C VAL d 330 " pdb=" CB VAL d 330 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" C3' U 7 2 " pdb=" C4' U 7 2 " pdb=" O3' U 7 2 " pdb=" C2' U 7 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3132 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.48e-02 4.19e+01 pdb=" C ILE b 331 " -0.112 2.00e-02 2.50e+03 pdb=" O ILE b 331 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR b 332 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 331 " -0.028 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C ILE e 331 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE e 331 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR e 332 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 331 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE c 331 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE c 331 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR c 332 " 0.028 2.00e-02 2.50e+03 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 55 2.02 - 2.74: 1642 2.74 - 3.46: 29057 3.46 - 4.18: 46275 4.18 - 4.90: 83659 Nonbonded interactions: 160688 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 3.040 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 nonbonded pdb=" NH1 ARG e 272 " pdb=" OE2 GLU f 334 " model vdw 1.416 3.120 nonbonded pdb=" NZ LYS e 385 " pdb=" O LYS d 352 " model vdw 1.495 3.120 ... (remaining 160683 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' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.130 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3706 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 : 0.019 0.748 20401 Z= 1.843 Angle : 0.641 14.413 27503 Z= 0.352 Chirality : 0.042 0.258 3135 Planarity : 0.004 0.065 3525 Dihedral : 11.889 149.051 7951 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 4.11 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.83 (0.16), residues: 2490 helix: 0.26 (0.15), residues: 1134 sheet: -2.06 (0.22), residues: 378 loop : -0.69 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 366 TYR 0.016 0.001 TYR d 332 PHE 0.007 0.001 PHE a 36 TRP 0.003 0.001 TRP a 381 HIS 0.001 0.000 HIS e 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 (20371) covalent geometry : angle 0.64137 / 0.35 (27503) hydrogen bonds : bond 0.19912 / 14.19 ( 944) hydrogen bonds : angle 6.53638 / 5.15 ( 2742) Misc. bond : bond 0.47746 / 46.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.673 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.1134 (mmm) cc_final: -0.0696 (ttt) REVERT: c 29 MET cc_start: -0.1502 (mtp) cc_final: -0.2170 (ttt) REVERT: b 29 MET cc_start: -0.1529 (mtp) cc_final: -0.2116 (ttt) REVERT: d 21 MET cc_start: -0.0973 (mmm) cc_final: -0.4034 (ttt) outliers start: 35 outliers final: 8 residues processed: 269 average time/residue: 0.1677 time to fit residues: 67.1181 Evaluate side-chains 147 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 172 GLN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 220 GLN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.038748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.031320 restraints weight = 315663.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.031937 restraints weight = 245687.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.032394 restraints weight = 203118.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.032735 restraints weight = 175878.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.032980 restraints weight = 157529.703| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20401 Z= 0.260 Angle : 0.847 13.404 27503 Z= 0.406 Chirality : 0.046 0.280 3135 Planarity : 0.005 0.069 3525 Dihedral : 10.704 166.119 2917 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.14 (0.17), residues: 2490 helix: 0.72 (0.15), residues: 1128 sheet: -0.96 (0.23), residues: 438 loop : 0.10 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG c 212 TYR 0.030 0.002 TYR d 332 PHE 0.031 0.003 PHE b 335 TRP 0.007 0.002 TRP d 381 HIS 0.012 0.002 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (20371) covalent geometry : angle 0.84681 / 0.41 (27503) hydrogen bonds : bond 0.04343 / 3.08 ( 944) hydrogen bonds : angle 4.98397 / 3.90 ( 2742) Misc. bond : bond 0.00776 / 0.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.656 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: symmetry clash 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: symmetry clash REVERT: e 29 MET cc_start: 0.5106 (ttm) cc_final: 0.4689 (ttt) REVERT: f 21 MET cc_start: -0.2510 (mmm) cc_final: -0.3158 (mtm) REVERT: f 147 MET cc_start: 0.8639 (mmp) cc_final: 0.7996 (mtm) REVERT: f 219 MET cc_start: 0.9216 (mmp) cc_final: 0.8822 (mmm) REVERT: f 341 MET cc_start: 0.2844 (tmm) cc_final: 0.2398 (tmm) REVERT: c 1 MET cc_start: 0.8458 (mpp) cc_final: 0.8242 (mpp) REVERT: c 248 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9121 (mt-10) REVERT: b 111 PHE cc_start: 0.8737 (m-80) cc_final: 0.8090 (m-80) REVERT: b 396 MET cc_start: 0.8502 (mtt) cc_final: 0.8235 (mtt) REVERT: a 132 LEU cc_start: 0.9466 (mt) cc_final: 0.9222 (mt) REVERT: d 21 MET cc_start: -0.4518 (mmm) cc_final: -0.4783 (mtt) REVERT: d 29 MET cc_start: 0.8504 (ttp) cc_final: 0.8070 (ptm) REVERT: d 147 MET cc_start: 0.8484 (mmp) cc_final: 0.8173 (mmp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1349 time to fit residues: 33.8235 Evaluate side-chains 123 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 147 optimal weight: 0.0050 chunk 79 optimal weight: 2.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 340 ASN ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.039329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.031970 restraints weight = 311520.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.032622 restraints weight = 234523.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.033110 restraints weight = 189974.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.033473 restraints weight = 162690.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.033734 restraints weight = 144310.688| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20401 Z= 0.130 Angle : 0.654 8.468 27503 Z= 0.314 Chirality : 0.043 0.208 3135 Planarity : 0.004 0.046 3525 Dihedral : 10.603 166.518 2917 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.17), residues: 2490 helix: 0.78 (0.15), residues: 1146 sheet: -0.48 (0.24), residues: 438 loop : 0.30 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 212 TYR 0.015 0.001 TYR e 332 PHE 0.017 0.002 PHE a 413 TRP 0.009 0.001 TRP d 381 HIS 0.012 0.001 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20371) covalent geometry : angle 0.65354 / 0.31 (27503) hydrogen bonds : bond 0.03360 / 2.40 ( 944) hydrogen bonds : angle 4.68365 / 3.66 ( 2742) Misc. bond : bond 0.00294 / 0.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.636 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.1563 (ttt) cc_final: -0.1833 (ttt) REVERT: e 29 MET cc_start: 0.4508 (ttm) cc_final: 0.4093 (ttt) REVERT: e 207 LEU cc_start: 0.9239 (tt) cc_final: 0.8993 (mt) REVERT: f 21 MET cc_start: -0.2508 (mmm) cc_final: -0.3287 (mtm) REVERT: f 219 MET cc_start: 0.9188 (mmp) cc_final: 0.8767 (mmm) REVERT: c 248 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9084 (mt-10) REVERT: c 416 MET cc_start: 0.4765 (ptm) cc_final: 0.4540 (ptt) REVERT: b 29 MET cc_start: 0.1380 (ttt) cc_final: 0.1101 (ttt) REVERT: b 111 PHE cc_start: 0.8837 (m-80) cc_final: 0.8088 (m-80) REVERT: b 341 MET cc_start: 0.0680 (mmm) cc_final: -0.0251 (mmt) REVERT: b 396 MET cc_start: 0.8207 (mtt) cc_final: 0.7906 (mtt) REVERT: a 132 LEU cc_start: 0.9498 (mt) cc_final: 0.9278 (mt) REVERT: d 21 MET cc_start: -0.4543 (mmm) cc_final: -0.4801 (mtt) REVERT: d 29 MET cc_start: 0.8512 (ttp) cc_final: 0.8037 (ptm) REVERT: d 147 MET cc_start: 0.8525 (mmp) cc_final: 0.8212 (mmp) REVERT: d 219 MET cc_start: 0.9522 (mmp) cc_final: 0.9038 (mmt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1444 time to fit residues: 33.9026 Evaluate side-chains 122 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 117 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 135 ASN e 172 GLN e 220 GLN e 241 GLN e 256 HIS f 126 ASN f 135 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS c 25 ASN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 ASN b 25 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN b 241 GLN a 126 ASN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN a 256 HIS d 135 ASN d 172 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.034956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.027854 restraints weight = 332765.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.028428 restraints weight = 260376.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.028842 restraints weight = 216137.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.029155 restraints weight = 187957.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.029395 restraints weight = 168657.501| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20401 Z= 0.256 Angle : 0.831 9.390 27503 Z= 0.400 Chirality : 0.044 0.208 3135 Planarity : 0.005 0.049 3525 Dihedral : 10.661 165.676 2917 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.54 (0.17), residues: 2490 helix: 0.55 (0.15), residues: 1116 sheet: -0.16 (0.26), residues: 402 loop : 0.64 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 221 TYR 0.019 0.002 TYR d 332 PHE 0.064 0.003 PHE e 36 TRP 0.006 0.002 TRP b 381 HIS 0.009 0.002 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (20371) covalent geometry : angle 0.83086 / 0.40 (27503) hydrogen bonds : bond 0.03862 / 2.86 ( 944) hydrogen bonds : angle 4.68913 / 3.61 ( 2742) Misc. bond : bond 0.00362 / 0.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.819 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.8115 (pmm) cc_final: 0.7836 (pmm) REVERT: e 21 MET cc_start: -0.1338 (ttt) cc_final: -0.1584 (ttt) REVERT: e 245 MET cc_start: 0.8772 (ptp) cc_final: 0.8495 (ptt) REVERT: f 1 MET cc_start: 0.4035 (pmm) cc_final: 0.3577 (pmm) REVERT: f 21 MET cc_start: -0.1959 (mmm) cc_final: -0.2533 (mtt) REVERT: f 29 MET cc_start: 0.2220 (ttm) cc_final: 0.1961 (ptm) REVERT: f 219 MET cc_start: 0.9394 (mmp) cc_final: 0.8953 (mmm) REVERT: f 396 MET cc_start: 0.9284 (mmp) cc_final: 0.9047 (mmm) REVERT: c 147 MET cc_start: 0.5887 (tpt) cc_final: 0.4619 (mpp) REVERT: c 248 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9263 (mt-10) REVERT: c 390 MET cc_start: 0.7686 (ppp) cc_final: 0.6868 (ppp) REVERT: b 29 MET cc_start: 0.1359 (ttt) cc_final: 0.1075 (ttt) REVERT: b 111 PHE cc_start: 0.8974 (m-80) cc_final: 0.8401 (m-80) REVERT: b 341 MET cc_start: 0.1571 (mmm) cc_final: 0.0273 (mmt) REVERT: a 132 LEU cc_start: 0.9604 (mt) cc_final: 0.9376 (mt) REVERT: a 327 MET cc_start: 0.9430 (tmm) cc_final: 0.9203 (tpp) REVERT: d 21 MET cc_start: -0.4318 (mmm) cc_final: -0.4678 (mtt) REVERT: d 147 MET cc_start: 0.8585 (mmp) cc_final: 0.8263 (mmp) REVERT: d 219 MET cc_start: 0.9529 (mmp) cc_final: 0.9171 (mmt) REVERT: d 390 MET cc_start: 0.8503 (pmm) cc_final: 0.8258 (pmm) outliers start: 2 outliers final: 2 residues processed: 135 average time/residue: 0.1489 time to fit residues: 31.8814 Evaluate side-chains 115 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 81 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.034184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.027232 restraints weight = 334279.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.027816 restraints weight = 258359.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.028236 restraints weight = 212760.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.028557 restraints weight = 183949.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.028794 restraints weight = 164311.732| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20401 Z= 0.192 Angle : 0.689 7.976 27503 Z= 0.339 Chirality : 0.044 0.208 3135 Planarity : 0.004 0.044 3525 Dihedral : 10.633 168.879 2917 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.17), residues: 2490 helix: 0.61 (0.15), residues: 1164 sheet: -0.21 (0.26), residues: 402 loop : 0.36 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 221 TYR 0.017 0.002 TYR f 332 PHE 0.025 0.002 PHE f 412 TRP 0.005 0.001 TRP d 381 HIS 0.010 0.002 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (20371) covalent geometry : angle 0.68870 / 0.34 (27503) hydrogen bonds : bond 0.03417 / 2.51 ( 944) hydrogen bonds : angle 4.57824 / 3.53 ( 2742) Misc. bond : bond 0.00306 / 0.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.850 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: symmetry clash 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: symmetry clash REVERT: e 1 MET cc_start: 0.8222 (pmm) cc_final: 0.8011 (pmm) REVERT: e 21 MET cc_start: -0.1697 (ttt) cc_final: -0.1956 (ttt) REVERT: e 29 MET cc_start: 0.4737 (ttm) cc_final: 0.4291 (ttm) REVERT: f 1 MET cc_start: 0.4558 (pmm) cc_final: 0.4288 (pmm) REVERT: f 21 MET cc_start: -0.1344 (mmm) cc_final: -0.2019 (mtp) REVERT: f 29 MET cc_start: 0.2303 (ttm) cc_final: 0.1952 (ptm) REVERT: f 147 MET cc_start: 0.8481 (mmp) cc_final: 0.8096 (mpp) REVERT: f 219 MET cc_start: 0.9236 (mmp) cc_final: 0.8888 (mmm) REVERT: f 341 MET cc_start: 0.3623 (tmm) cc_final: 0.3304 (tmm) REVERT: f 396 MET cc_start: 0.9146 (mmp) cc_final: 0.8929 (mmm) REVERT: c 147 MET cc_start: 0.5608 (tpt) cc_final: 0.4800 (mpp) REVERT: c 390 MET cc_start: 0.7342 (ppp) cc_final: 0.6586 (ppp) REVERT: b 29 MET cc_start: 0.1508 (ttt) cc_final: 0.1257 (ttt) REVERT: b 111 PHE cc_start: 0.8856 (m-80) cc_final: 0.8295 (m-80) REVERT: b 207 LEU cc_start: 0.9261 (mp) cc_final: 0.8991 (mp) REVERT: d 21 MET cc_start: -0.4106 (mmm) cc_final: -0.4415 (mtm) REVERT: d 29 MET cc_start: 0.8880 (ttp) cc_final: 0.8398 (ptm) REVERT: d 147 MET cc_start: 0.8591 (mmp) cc_final: 0.7760 (tpt) REVERT: d 219 MET cc_start: 0.9551 (mmp) cc_final: 0.9244 (mmm) REVERT: d 390 MET cc_start: 0.8552 (pmm) cc_final: 0.8144 (pmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1380 time to fit residues: 28.1660 Evaluate side-chains 112 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 175 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 147 optimal weight: 0.0060 chunk 80 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 25 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.033951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.027032 restraints weight = 332441.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.027612 restraints weight = 256134.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.028036 restraints weight = 210995.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.028353 restraints weight = 182193.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.028585 restraints weight = 162553.504| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20401 Z= 0.160 Angle : 0.674 9.401 27503 Z= 0.322 Chirality : 0.043 0.316 3135 Planarity : 0.004 0.056 3525 Dihedral : 10.629 168.703 2917 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.05 % Allowed : 1.63 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.55 (0.17), residues: 2490 helix: 0.74 (0.15), residues: 1164 sheet: -0.38 (0.27), residues: 390 loop : 0.48 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG c 366 TYR 0.042 0.002 TYR b 332 PHE 0.024 0.002 PHE f 412 TRP 0.005 0.001 TRP d 381 HIS 0.012 0.001 HIS b 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (20371) covalent geometry : angle 0.67449 / 0.32 (27503) hydrogen bonds : bond 0.03082 / 2.24 ( 944) hydrogen bonds : angle 4.45179 / 3.44 ( 2742) Misc. bond : bond 0.00500 / 0.42 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.931 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.8371 (pmm) cc_final: 0.8034 (pmm) REVERT: e 21 MET cc_start: -0.1394 (ttt) cc_final: -0.1638 (ttt) REVERT: e 29 MET cc_start: 0.4803 (ttm) cc_final: 0.4371 (ttm) REVERT: f 1 MET cc_start: 0.4702 (pmm) cc_final: 0.4095 (pmm) REVERT: f 21 MET cc_start: -0.1017 (mmm) cc_final: -0.1747 (mtt) REVERT: f 29 MET cc_start: 0.2345 (ttm) cc_final: 0.2033 (ptm) REVERT: f 219 MET cc_start: 0.9242 (mmp) cc_final: 0.8809 (mmm) REVERT: f 341 MET cc_start: 0.3718 (tmm) cc_final: 0.3347 (tmm) REVERT: f 396 MET cc_start: 0.9161 (mmp) cc_final: 0.8791 (mtp) REVERT: c 245 MET cc_start: 0.8172 (ptt) cc_final: 0.6983 (ptt) REVERT: c 380 MET cc_start: 0.9049 (mmt) cc_final: 0.8791 (mmt) REVERT: c 390 MET cc_start: 0.7651 (ppp) cc_final: 0.6800 (ppp) REVERT: b 29 MET cc_start: 0.1444 (ttt) cc_final: 0.1144 (ttt) REVERT: b 111 PHE cc_start: 0.8882 (m-80) cc_final: 0.8364 (m-80) REVERT: a 29 MET cc_start: 0.2715 (ttm) cc_final: 0.2467 (ttm) REVERT: a 132 LEU cc_start: 0.9641 (mt) cc_final: 0.9436 (mt) REVERT: d 21 MET cc_start: -0.3794 (mmm) cc_final: -0.4103 (mtt) REVERT: d 29 MET cc_start: 0.8842 (ttp) cc_final: 0.8338 (ptm) REVERT: d 147 MET cc_start: 0.8570 (mmp) cc_final: 0.7764 (tpt) REVERT: d 219 MET cc_start: 0.9558 (mmp) cc_final: 0.9263 (mmm) REVERT: d 341 MET cc_start: -0.0718 (mmm) cc_final: -0.1043 (mmm) REVERT: d 390 MET cc_start: 0.8372 (pmm) cc_final: 0.8037 (pmm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1370 time to fit residues: 28.5212 Evaluate side-chains 116 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 188 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.034105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.027180 restraints weight = 331141.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.027770 restraints weight = 253410.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.028197 restraints weight = 207760.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.028516 restraints weight = 179036.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.028752 restraints weight = 159462.362| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20401 Z= 0.128 Angle : 0.641 10.843 27503 Z= 0.305 Chirality : 0.043 0.350 3135 Planarity : 0.004 0.045 3525 Dihedral : 10.460 165.345 2917 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.68 (0.17), residues: 2490 helix: 0.84 (0.15), residues: 1170 sheet: -0.42 (0.26), residues: 390 loop : 0.61 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 366 TYR 0.016 0.001 TYR b 332 PHE 0.018 0.001 PHE f 412 TRP 0.007 0.001 TRP d 381 HIS 0.013 0.001 HIS c 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (20371) covalent geometry : angle 0.64096 / 0.31 (27503) hydrogen bonds : bond 0.02940 / 2.14 ( 944) hydrogen bonds : angle 4.38537 / 3.40 ( 2742) Misc. bond : bond 0.00455 / 0.42 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.864 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: symmetry clash 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: symmetry clash REVERT: e 1 MET cc_start: 0.8388 (pmm) cc_final: 0.8172 (pmm) REVERT: e 29 MET cc_start: 0.4736 (ttm) cc_final: 0.4318 (ttm) REVERT: f 1 MET cc_start: 0.4875 (pmm) cc_final: 0.4243 (pmm) REVERT: f 21 MET cc_start: -0.1114 (mmm) cc_final: -0.2005 (mtt) REVERT: f 219 MET cc_start: 0.9220 (mmp) cc_final: 0.8878 (mmm) REVERT: f 341 MET cc_start: 0.3689 (tmm) cc_final: 0.3280 (tmm) REVERT: f 396 MET cc_start: 0.9161 (mmp) cc_final: 0.8779 (mtp) REVERT: c 390 MET cc_start: 0.7677 (ppp) cc_final: 0.6817 (ppp) REVERT: b 29 MET cc_start: 0.1558 (ttt) cc_final: 0.1202 (ttt) REVERT: b 111 PHE cc_start: 0.8889 (m-80) cc_final: 0.8354 (m-80) REVERT: b 207 LEU cc_start: 0.9367 (mp) cc_final: 0.9097 (mp) REVERT: b 341 MET cc_start: 0.2177 (mmm) cc_final: 0.1964 (mmm) REVERT: a 1 MET cc_start: 0.7376 (pmm) cc_final: 0.7087 (pmm) REVERT: a 245 MET cc_start: 0.9334 (pmm) cc_final: 0.9002 (pmm) REVERT: d 21 MET cc_start: -0.3823 (mmm) cc_final: -0.4099 (mtt) REVERT: d 29 MET cc_start: 0.8823 (ttp) cc_final: 0.8335 (ptm) REVERT: d 147 MET cc_start: 0.8581 (mmp) cc_final: 0.7748 (tpt) REVERT: d 219 MET cc_start: 0.9566 (mmp) cc_final: 0.9266 (mmm) REVERT: d 390 MET cc_start: 0.8464 (pmm) cc_final: 0.8103 (pmm) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1373 time to fit residues: 27.7689 Evaluate side-chains 112 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 33 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 126 ASN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 HIS a 25 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.032829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.026023 restraints weight = 340041.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.026582 restraints weight = 261653.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.026998 restraints weight = 214907.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.027303 restraints weight = 185071.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.027537 restraints weight = 165429.716| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20401 Z= 0.171 Angle : 0.678 8.537 27503 Z= 0.326 Chirality : 0.043 0.231 3135 Planarity : 0.004 0.047 3525 Dihedral : 10.447 163.306 2917 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.59 (0.17), residues: 2490 helix: 0.75 (0.15), residues: 1176 sheet: -0.46 (0.26), residues: 390 loop : 0.59 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 221 TYR 0.015 0.002 TYR d 332 PHE 0.029 0.002 PHE f 412 TRP 0.005 0.001 TRP d 381 HIS 0.010 0.002 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (20371) covalent geometry : angle 0.67831 / 0.33 (27503) hydrogen bonds : bond 0.03113 / 2.30 ( 944) hydrogen bonds : angle 4.43755 / 3.44 ( 2742) Misc. bond : bond 0.00419 / 0.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.794 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: symmetry clash 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: symmetry clash REVERT: e 1 MET cc_start: 0.8527 (pmm) cc_final: 0.8183 (pmm) REVERT: e 21 MET cc_start: -0.1296 (ttt) cc_final: -0.1619 (ttt) REVERT: f 1 MET cc_start: 0.5003 (pmm) cc_final: 0.4388 (pmm) REVERT: f 21 MET cc_start: -0.1111 (mmm) cc_final: -0.2192 (mtt) REVERT: f 29 MET cc_start: 0.1679 (ttp) cc_final: 0.1232 (tmm) REVERT: f 219 MET cc_start: 0.9211 (mmp) cc_final: 0.8756 (mmm) REVERT: f 341 MET cc_start: 0.4244 (tmm) cc_final: 0.3800 (tmm) REVERT: f 396 MET cc_start: 0.9174 (mmp) cc_final: 0.8827 (mtp) REVERT: c 245 MET cc_start: 0.8013 (ptt) cc_final: 0.7804 (ptt) REVERT: c 380 MET cc_start: 0.9060 (mmt) cc_final: 0.8802 (mmt) REVERT: c 390 MET cc_start: 0.7808 (ppp) cc_final: 0.7098 (ppp) REVERT: b 29 MET cc_start: 0.1941 (ttt) cc_final: 0.1500 (ttt) REVERT: b 72 TYR cc_start: 0.9121 (m-80) cc_final: 0.8855 (m-10) REVERT: b 111 PHE cc_start: 0.8911 (m-80) cc_final: 0.8414 (m-80) REVERT: b 147 MET cc_start: 0.5085 (tpt) cc_final: 0.4729 (mpp) REVERT: b 341 MET cc_start: 0.2495 (mmm) cc_final: 0.2230 (mmm) REVERT: a 1 MET cc_start: 0.7318 (pmm) cc_final: 0.6869 (pmm) REVERT: a 29 MET cc_start: 0.2348 (ttp) cc_final: 0.1752 (tmm) REVERT: a 245 MET cc_start: 0.9330 (pmm) cc_final: 0.9015 (pmm) REVERT: d 21 MET cc_start: -0.3679 (mmm) cc_final: -0.3952 (mtt) REVERT: d 147 MET cc_start: 0.8489 (mmp) cc_final: 0.7696 (tpt) REVERT: d 219 MET cc_start: 0.9598 (mmp) cc_final: 0.9333 (mmm) REVERT: d 390 MET cc_start: 0.8534 (pmm) cc_final: 0.8185 (pmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1399 time to fit residues: 28.2600 Evaluate side-chains 108 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 29 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 ASN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.031894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.025226 restraints weight = 342999.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.025790 restraints weight = 262203.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.026200 restraints weight = 213488.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.026498 restraints weight = 183447.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.026727 restraints weight = 163652.171| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20401 Z= 0.180 Angle : 0.700 8.995 27503 Z= 0.340 Chirality : 0.043 0.242 3135 Planarity : 0.004 0.046 3525 Dihedral : 10.460 163.845 2917 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.46 (0.17), residues: 2490 helix: 0.60 (0.14), residues: 1182 sheet: -0.49 (0.26), residues: 390 loop : 0.57 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG f 92 TYR 0.044 0.002 TYR c 332 PHE 0.014 0.002 PHE f 412 TRP 0.004 0.001 TRP d 381 HIS 0.022 0.002 HIS c 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (20371) covalent geometry : angle 0.70034 / 0.34 (27503) hydrogen bonds : bond 0.03262 / 2.41 ( 944) hydrogen bonds : angle 4.52175 / 3.55 ( 2742) Misc. bond : bond 0.00398 / 0.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.004 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: symmetry clash 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: e 1 MET cc_start: 0.8415 (pmm) cc_final: 0.8020 (pmm) REVERT: e 21 MET cc_start: -0.1328 (ttt) cc_final: -0.1558 (ttt) REVERT: e 29 MET cc_start: 0.5044 (ttm) cc_final: 0.4345 (ttp) REVERT: e 186 MET cc_start: 0.9181 (ptp) cc_final: 0.8934 (pmm) REVERT: e 341 MET cc_start: -0.0832 (mpp) cc_final: -0.1102 (mpp) REVERT: f 1 MET cc_start: 0.5159 (pmm) cc_final: 0.4621 (pmm) REVERT: f 21 MET cc_start: -0.0720 (mmm) cc_final: -0.2069 (mtt) REVERT: f 29 MET cc_start: 0.1878 (ttp) cc_final: 0.1354 (tmm) REVERT: f 219 MET cc_start: 0.9197 (mmp) cc_final: 0.8848 (mmm) REVERT: f 341 MET cc_start: 0.4648 (tmm) cc_final: 0.4104 (tmm) REVERT: f 396 MET cc_start: 0.9170 (mmp) cc_final: 0.8821 (mtp) REVERT: f 415 MET cc_start: 0.9117 (mpp) cc_final: 0.8753 (ptp) REVERT: c 147 MET cc_start: 0.5903 (tpt) cc_final: 0.5150 (mpp) REVERT: c 245 MET cc_start: 0.8277 (ptt) cc_final: 0.8051 (ptt) REVERT: c 380 MET cc_start: 0.9042 (mmt) cc_final: 0.8838 (mmt) REVERT: c 390 MET cc_start: 0.7866 (ppp) cc_final: 0.7277 (ppp) REVERT: b 29 MET cc_start: 0.2047 (ttt) cc_final: 0.1755 (ttt) REVERT: b 72 TYR cc_start: 0.9118 (m-80) cc_final: 0.8830 (m-10) REVERT: b 111 PHE cc_start: 0.8950 (m-80) cc_final: 0.8434 (m-80) REVERT: b 147 MET cc_start: 0.5213 (tpt) cc_final: 0.4970 (mpp) REVERT: a 1 MET cc_start: 0.7185 (pmm) cc_final: 0.6604 (pmm) REVERT: a 245 MET cc_start: 0.9352 (pmm) cc_final: 0.8374 (pmm) REVERT: a 396 MET cc_start: 0.8581 (mtt) cc_final: 0.8072 (mmp) REVERT: d 21 MET cc_start: -0.3528 (mmm) cc_final: -0.3752 (mtt) REVERT: d 29 MET cc_start: 0.8790 (ttp) cc_final: 0.8487 (ptm) REVERT: d 147 MET cc_start: 0.8302 (mmp) cc_final: 0.7552 (tpt) REVERT: d 219 MET cc_start: 0.9553 (mmp) cc_final: 0.9278 (mmm) REVERT: d 341 MET cc_start: 0.0906 (mmp) cc_final: -0.0163 (tpp) REVERT: d 390 MET cc_start: 0.8577 (pmm) cc_final: 0.8254 (pmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1414 time to fit residues: 28.0940 Evaluate side-chains 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 156 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.032088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.025449 restraints weight = 339973.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.026026 restraints weight = 257276.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.026447 restraints weight = 209031.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.026759 restraints weight = 178840.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.026994 restraints weight = 158663.669| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20401 Z= 0.137 Angle : 0.661 8.280 27503 Z= 0.317 Chirality : 0.043 0.250 3135 Planarity : 0.004 0.047 3525 Dihedral : 10.423 162.060 2917 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.58 (0.17), residues: 2490 helix: 0.73 (0.15), residues: 1182 sheet: -0.48 (0.26), residues: 390 loop : 0.63 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 366 TYR 0.019 0.002 TYR c 332 PHE 0.016 0.001 PHE f 412 TRP 0.005 0.001 TRP d 381 HIS 0.010 0.001 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (20371) covalent geometry : angle 0.66056 / 0.32 (27503) hydrogen bonds : bond 0.03094 / 2.24 ( 944) hydrogen bonds : angle 4.47526 / 3.48 ( 2742) Misc. bond : bond 0.00346 / 0.33 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.645 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: symmetry clash 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: symmetry clash REVERT: e 1 MET cc_start: 0.8329 (pmm) cc_final: 0.7964 (pmm) REVERT: e 21 MET cc_start: -0.1243 (ttt) cc_final: -0.1547 (ttt) REVERT: e 29 MET cc_start: 0.4987 (ttm) cc_final: 0.4361 (ttp) REVERT: e 327 MET cc_start: 0.9621 (tmm) cc_final: 0.9405 (tmm) REVERT: e 341 MET cc_start: -0.0997 (mpp) cc_final: -0.1237 (mpp) REVERT: f 21 MET cc_start: -0.0464 (mmm) cc_final: -0.1812 (mtm) REVERT: f 29 MET cc_start: 0.1770 (ttp) cc_final: 0.1346 (tmm) REVERT: f 219 MET cc_start: 0.9162 (mmp) cc_final: 0.8672 (mmp) REVERT: f 396 MET cc_start: 0.9195 (mmp) cc_final: 0.8833 (mtp) REVERT: f 415 MET cc_start: 0.9216 (mpp) cc_final: 0.8868 (ptp) REVERT: c 380 MET cc_start: 0.9100 (mmt) cc_final: 0.8885 (mmt) REVERT: c 390 MET cc_start: 0.8028 (ppp) cc_final: 0.7420 (ppp) REVERT: b 29 MET cc_start: 0.2251 (ttt) cc_final: 0.1949 (ttt) REVERT: b 111 PHE cc_start: 0.8939 (m-80) cc_final: 0.8404 (m-80) REVERT: a 1 MET cc_start: 0.7001 (pmm) cc_final: 0.6524 (pmm) REVERT: a 396 MET cc_start: 0.8557 (mtt) cc_final: 0.8038 (mmp) REVERT: d 29 MET cc_start: 0.8731 (ttp) cc_final: 0.8397 (ptm) REVERT: d 147 MET cc_start: 0.8352 (mmp) cc_final: 0.7617 (tpt) REVERT: d 219 MET cc_start: 0.9579 (mmp) cc_final: 0.9298 (mmm) REVERT: d 341 MET cc_start: 0.0813 (mmp) cc_final: -0.0203 (tpp) REVERT: d 390 MET cc_start: 0.8564 (pmm) cc_final: 0.8231 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1253 time to fit residues: 24.3580 Evaluate side-chains 108 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 49 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.032190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.025558 restraints weight = 339476.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.026146 restraints weight = 255647.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.026571 restraints weight = 207003.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.026889 restraints weight = 176815.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.027119 restraints weight = 156419.969| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20401 Z= 0.123 Angle : 0.649 12.800 27503 Z= 0.311 Chirality : 0.043 0.248 3135 Planarity : 0.003 0.045 3525 Dihedral : 10.337 161.488 2917 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.69 (0.17), residues: 2490 helix: 0.85 (0.15), residues: 1164 sheet: -0.45 (0.26), residues: 390 loop : 0.64 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 366 TYR 0.018 0.001 TYR d 332 PHE 0.015 0.001 PHE f 412 TRP 0.007 0.001 TRP d 381 HIS 0.009 0.001 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (20371) covalent geometry : angle 0.64851 / 0.31 (27503) hydrogen bonds : bond 0.02938 / 2.13 ( 944) hydrogen bonds : angle 4.42731 / 3.45 ( 2742) Misc. bond : bond 0.00346 / 0.32 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.77 seconds wall clock time: 56 minutes 56.50 seconds (3416.50 seconds total)