Starting phenix.real_space_refine on Fri Aug 7 07:59:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5l_27914/08_2026/8e5l_27914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5l_27914/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2026/8e5l_27914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2026/8e5l_27914_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2026/8e5l_27914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2026/8e5l_27914.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.33, per 1000 atoms: 0.17 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: 1.23 Conformation dependent library (CDL) restraints added in 682.9 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: 0.51 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: 2.74 Time building geometry restraints manager: 1.67 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: 413 0.103 - 0.155: 114 0.155 - 0.206: 7 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- 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 : 0.041 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 0.64132 / 0.35 (27503) hydrogen bonds : bond 0.19912 / 14.68 ( 944) hydrogen bonds : angle 6.53638 / 5.15 ( 2742) Misc. bond : bond 0.47746 / 50.34 ( 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 : 0.588 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: 0.1285 time to fit residues: 51.3991 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 : 0.692 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.038715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.031290 restraints weight = 315836.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.031907 restraints weight = 245799.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.032358 restraints weight = 203365.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.032701 restraints weight = 176246.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.032948 restraints weight = 157653.093| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20401 Z= 0.253 Angle : 0.838 12.055 27503 Z= 0.402 Chirality : 0.046 0.294 3135 Planarity : 0.005 0.065 3525 Dihedral : 10.696 166.653 2917 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 0.11 (0.17), residues: 2490 helix: 0.69 (0.15), residues: 1128 sheet: -1.00 (0.23), residues: 438 loop : 0.09 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 212 TYR 0.025 0.002 TYR d 332 PHE 0.038 0.003 PHE b 335 TRP 0.007 0.002 TRP f 381 HIS 0.013 0.002 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 (20371) covalent geometry : angle 0.83803 / 0.40 (27503) hydrogen bonds : bond 0.04446 / 3.28 ( 944) hydrogen bonds : angle 4.99546 / 3.93 ( 2742) Misc. bond : bond 0.00905 / 0.97 ( 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 : 0.509 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: e 29 MET cc_start: 0.5104 (ttm) cc_final: 0.4688 (ttt) REVERT: e 207 LEU cc_start: 0.9256 (mp) cc_final: 0.8954 (mp) REVERT: e 327 MET cc_start: 0.9655 (tmm) cc_final: 0.9396 (tmm) REVERT: f 21 MET cc_start: -0.2501 (mmm) cc_final: -0.3145 (mtm) REVERT: f 147 MET cc_start: 0.8640 (mmp) cc_final: 0.7997 (mtm) REVERT: f 219 MET cc_start: 0.9236 (mmp) cc_final: 0.8845 (mmm) REVERT: f 341 MET cc_start: 0.2854 (tmm) cc_final: 0.2401 (tmm) REVERT: c 1 MET cc_start: 0.8475 (mpp) cc_final: 0.8260 (mpp) REVERT: c 248 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9125 (mt-10) REVERT: b 111 PHE cc_start: 0.8736 (m-80) cc_final: 0.8078 (m-80) REVERT: a 132 LEU cc_start: 0.9504 (mt) cc_final: 0.9291 (mt) REVERT: d 21 MET cc_start: -0.4514 (mmm) cc_final: -0.4778 (mtt) REVERT: d 29 MET cc_start: 0.8551 (ttp) cc_final: 0.8137 (ptm) REVERT: d 147 MET cc_start: 0.8478 (mmp) cc_final: 0.8170 (mmp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1124 time to fit residues: 28.1217 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 : 0.748 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 188 optimal weight: 0.0000 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 147 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 overall best weight: 1.8148 ------------------------------------------------------------------------------- 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 25 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.038778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.031402 restraints weight = 313156.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.032056 restraints weight = 238651.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.032537 restraints weight = 195167.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.032898 restraints weight = 167362.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.033094 restraints weight = 148573.126| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20401 Z= 0.135 Angle : 0.649 8.197 27503 Z= 0.312 Chirality : 0.043 0.217 3135 Planarity : 0.004 0.041 3525 Dihedral : 10.583 166.100 2917 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.45 (0.17), residues: 2490 helix: 0.80 (0.16), residues: 1146 sheet: -0.47 (0.24), residues: 438 loop : 0.31 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 30 TYR 0.014 0.001 TYR e 332 PHE 0.016 0.002 PHE b 335 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 0.00291 / 0.13 (20371) covalent geometry : angle 0.64935 / 0.31 (27503) hydrogen bonds : bond 0.03344 / 2.47 ( 944) hydrogen bonds : angle 4.65707 / 3.64 ( 2742) Misc. bond : bond 0.00285 / 0.32 ( 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 147 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.649 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: e 21 MET cc_start: -0.1252 (ttt) cc_final: -0.1575 (ttt) REVERT: e 29 MET cc_start: 0.4869 (ttm) cc_final: 0.4458 (ttt) REVERT: f 21 MET cc_start: -0.2478 (mmm) cc_final: -0.3252 (mtm) REVERT: f 219 MET cc_start: 0.9268 (mmp) cc_final: 0.8836 (mmm) REVERT: c 1 MET cc_start: 0.8613 (mpp) cc_final: 0.8396 (mpp) REVERT: c 205 MET cc_start: 0.8816 (mtp) cc_final: 0.8527 (tpt) REVERT: c 207 LEU cc_start: 0.9405 (tt) cc_final: 0.9197 (tt) REVERT: c 248 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9093 (mt-10) REVERT: c 416 MET cc_start: 0.4820 (ptm) cc_final: 0.4585 (ptt) REVERT: b 29 MET cc_start: 0.1638 (ttt) cc_final: 0.1354 (ttt) REVERT: b 111 PHE cc_start: 0.8866 (m-80) cc_final: 0.8145 (m-80) REVERT: b 341 MET cc_start: 0.0601 (mmm) cc_final: -0.0355 (mmt) REVERT: a 132 LEU cc_start: 0.9514 (mt) cc_final: 0.9295 (mt) REVERT: d 21 MET cc_start: -0.4495 (mmm) cc_final: -0.4745 (mtt) REVERT: d 29 MET cc_start: 0.8583 (ttp) cc_final: 0.8117 (ptm) REVERT: d 147 MET cc_start: 0.8488 (mmp) cc_final: 0.8186 (mmp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1146 time to fit residues: 27.0337 Evaluate side-chains 120 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 134 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 32 GLN e 135 ASN e 241 GLN f 126 ASN f 135 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 241 GLN a 135 ASN d 135 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.036854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.029621 restraints weight = 322140.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.030240 restraints weight = 248980.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.030683 restraints weight = 204476.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.031022 restraints weight = 176770.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.031271 restraints weight = 157662.371| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3741 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= 0.170 Angle : 0.676 8.054 27503 Z= 0.326 Chirality : 0.042 0.208 3135 Planarity : 0.004 0.047 3525 Dihedral : 10.549 165.830 2917 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 0.70 (0.17), residues: 2490 helix: 0.89 (0.16), residues: 1140 sheet: -0.27 (0.25), residues: 402 loop : 0.52 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 212 TYR 0.015 0.001 TYR f 332 PHE 0.056 0.002 PHE f 36 TRP 0.008 0.001 TRP d 381 HIS 0.009 0.001 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (20371) covalent geometry : angle 0.67622 / 0.33 (27503) hydrogen bonds : bond 0.03223 / 2.37 ( 944) hydrogen bonds : angle 4.47157 / 3.49 ( 2742) Misc. bond : bond 0.00329 / 0.35 ( 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: 1 poor density : 134 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.1325 (ttt) cc_final: -0.1580 (ttt) REVERT: e 29 MET cc_start: 0.4853 (ttm) cc_final: 0.4402 (ttt) REVERT: e 207 LEU cc_start: 0.9253 (tt) cc_final: 0.9033 (mt) REVERT: f 21 MET cc_start: -0.2377 (mmm) cc_final: -0.3091 (mtm) REVERT: f 219 MET cc_start: 0.9336 (mmp) cc_final: 0.8940 (mmm) REVERT: c 1 MET cc_start: 0.8774 (mpp) cc_final: 0.8519 (mpp) REVERT: c 205 MET cc_start: 0.8896 (mtp) cc_final: 0.8637 (tpt) REVERT: c 390 MET cc_start: 0.7780 (ptt) cc_final: 0.7449 (ptm) REVERT: c 416 MET cc_start: 0.4829 (ptm) cc_final: 0.4445 (ptt) REVERT: b 111 PHE cc_start: 0.8961 (m-80) cc_final: 0.8312 (m-80) REVERT: b 207 LEU cc_start: 0.9293 (mp) cc_final: 0.8918 (mp) REVERT: b 245 MET cc_start: 0.8613 (ptp) cc_final: 0.8221 (ptp) REVERT: b 341 MET cc_start: 0.0964 (mmm) cc_final: -0.0315 (mmt) REVERT: a 341 MET cc_start: 0.1197 (mmm) cc_final: 0.0987 (mmm) REVERT: d 21 MET cc_start: -0.4487 (mmm) cc_final: -0.4692 (mtt) REVERT: d 147 MET cc_start: 0.8593 (mmp) cc_final: 0.8271 (mmp) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1149 time to fit residues: 25.2788 Evaluate side-chains 119 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 220 GLN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 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 = 0.3528 r_free = 0.3528 target = 0.036651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.029516 restraints weight = 320898.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.030124 restraints weight = 245618.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.030583 restraints weight = 201522.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.030921 restraints weight = 173308.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.031174 restraints weight = 154239.720| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20401 Z= 0.127 Angle : 0.612 7.887 27503 Z= 0.293 Chirality : 0.042 0.199 3135 Planarity : 0.004 0.045 3525 Dihedral : 10.435 165.694 2917 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 0.78 (0.17), residues: 2490 helix: 0.84 (0.15), residues: 1182 sheet: -0.13 (0.26), residues: 402 loop : 0.68 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 238 TYR 0.018 0.001 TYR f 332 PHE 0.031 0.002 PHE f 412 TRP 0.007 0.001 TRP d 381 HIS 0.007 0.001 HIS c 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (20371) covalent geometry : angle 0.61223 / 0.29 (27503) hydrogen bonds : bond 0.02860 / 2.14 ( 944) hydrogen bonds : angle 4.34005 / 3.39 ( 2742) Misc. bond : bond 0.00283 / 0.29 ( 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 136 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.502 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: e 29 MET cc_start: 0.4842 (ttm) cc_final: 0.4349 (ttt) REVERT: e 205 MET cc_start: 0.7714 (tmm) cc_final: 0.6964 (tmm) REVERT: e 245 MET cc_start: 0.8591 (ptp) cc_final: 0.8221 (ptt) REVERT: f 21 MET cc_start: -0.1815 (mmm) cc_final: -0.2602 (mtm) REVERT: f 29 MET cc_start: 0.1316 (ttp) cc_final: 0.0720 (tmm) REVERT: f 219 MET cc_start: 0.9285 (mmp) cc_final: 0.8854 (mmm) REVERT: c 1 MET cc_start: 0.8795 (mpp) cc_final: 0.8579 (mpp) REVERT: c 205 MET cc_start: 0.8892 (mtp) cc_final: 0.8626 (tpt) REVERT: c 248 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9232 (mt-10) REVERT: b 111 PHE cc_start: 0.8957 (m-80) cc_final: 0.8296 (m-80) REVERT: b 207 LEU cc_start: 0.9310 (mp) cc_final: 0.8958 (mp) REVERT: b 245 MET cc_start: 0.8398 (ptp) cc_final: 0.8073 (ptp) REVERT: a 132 LEU cc_start: 0.9598 (mt) cc_final: 0.9391 (mt) REVERT: d 21 MET cc_start: -0.4400 (mmm) cc_final: -0.4741 (mtt) REVERT: d 29 MET cc_start: 0.8670 (ttp) cc_final: 0.8149 (ptm) REVERT: d 147 MET cc_start: 0.8575 (mmp) cc_final: 0.8272 (mmp) REVERT: d 390 MET cc_start: 0.8357 (pmm) cc_final: 0.8025 (pmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1075 time to fit residues: 23.8168 Evaluate side-chains 120 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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: 7.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 80 optimal weight: 0.0670 chunk 155 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 137 optimal weight: 0.1980 chunk 168 optimal weight: 1.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.037184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.030077 restraints weight = 317534.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.030724 restraints weight = 240340.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.031190 restraints weight = 195274.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.031533 restraints weight = 166940.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.031789 restraints weight = 148167.668| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20401 Z= 0.108 Angle : 0.605 8.404 27503 Z= 0.285 Chirality : 0.043 0.274 3135 Planarity : 0.004 0.057 3525 Dihedral : 10.398 168.605 2917 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 0.94 (0.17), residues: 2490 helix: 0.96 (0.15), residues: 1182 sheet: -0.12 (0.26), residues: 402 loop : 0.81 (0.23), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG c 366 TYR 0.011 0.001 TYR e 332 PHE 0.020 0.001 PHE f 36 TRP 0.009 0.001 TRP d 381 HIS 0.007 0.001 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (20371) covalent geometry : angle 0.60521 / 0.29 (27503) hydrogen bonds : bond 0.02712 / 2.02 ( 944) hydrogen bonds : angle 4.26884 / 3.37 ( 2742) Misc. bond : bond 0.00434 / 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 134 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.528 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: e 21 MET cc_start: -0.1465 (ttt) cc_final: -0.1741 (ttt) REVERT: e 29 MET cc_start: 0.4705 (ttm) cc_final: 0.4240 (ttt) REVERT: f 1 MET cc_start: 0.3352 (pmm) cc_final: 0.2971 (pmm) REVERT: f 21 MET cc_start: -0.1538 (mmm) cc_final: -0.2348 (mtm) REVERT: f 29 MET cc_start: 0.1235 (ttp) cc_final: 0.0632 (tmm) REVERT: f 219 MET cc_start: 0.9264 (mmp) cc_final: 0.8841 (mmm) REVERT: c 1 MET cc_start: 0.8835 (mpp) cc_final: 0.8588 (mpp) REVERT: c 205 MET cc_start: 0.8961 (mtp) cc_final: 0.8663 (tpt) REVERT: c 248 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9229 (mt-10) REVERT: b 111 PHE cc_start: 0.8917 (m-80) cc_final: 0.8228 (m-80) REVERT: b 207 LEU cc_start: 0.9291 (mp) cc_final: 0.8891 (mp) REVERT: b 245 MET cc_start: 0.8457 (ptp) cc_final: 0.7935 (ptp) REVERT: b 341 MET cc_start: 0.1407 (mmm) cc_final: 0.0996 (mmm) REVERT: a 132 LEU cc_start: 0.9615 (mt) cc_final: 0.9402 (mt) REVERT: d 21 MET cc_start: -0.4255 (mmm) cc_final: -0.4592 (mtt) REVERT: d 29 MET cc_start: 0.8663 (ttp) cc_final: 0.8092 (ptm) REVERT: d 147 MET cc_start: 0.8535 (mmp) cc_final: 0.7690 (tpt) REVERT: d 390 MET cc_start: 0.8379 (pmm) cc_final: 0.7975 (pmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1186 time to fit residues: 25.8582 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 : 0.652 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 105 optimal weight: 0.0670 chunk 15 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 239 HIS e 241 GLN e 256 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS c 135 ASN ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN b 256 HIS a 126 ASN a 256 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.034313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.027300 restraints weight = 334017.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.027865 restraints weight = 259108.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.028283 restraints weight = 214243.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.028594 restraints weight = 185360.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.028824 restraints weight = 166167.069| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20401 Z= 0.204 Angle : 0.725 8.153 27503 Z= 0.350 Chirality : 0.043 0.243 3135 Planarity : 0.004 0.045 3525 Dihedral : 10.399 162.194 2917 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.80 (0.15), residues: 1170 sheet: -0.20 (0.26), residues: 396 loop : 0.59 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 221 TYR 0.032 0.002 TYR b 332 PHE 0.030 0.002 PHE f 412 TRP 0.004 0.001 TRP e 381 HIS 0.019 0.002 HIS b 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (20371) covalent geometry : angle 0.72532 / 0.35 (27503) hydrogen bonds : bond 0.03287 / 2.51 ( 944) hydrogen bonds : angle 4.38464 / 3.38 ( 2742) Misc. bond : bond 0.00391 / 0.35 ( 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 129 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.604 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: 0.8229 (pmm) cc_final: 0.7855 (pmm) REVERT: e 21 MET cc_start: -0.1207 (ttt) cc_final: -0.1464 (ttt) REVERT: e 29 MET cc_start: 0.5122 (ttm) cc_final: 0.4806 (ttm) REVERT: f 1 MET cc_start: 0.3955 (pmm) cc_final: 0.3565 (pmm) REVERT: f 21 MET cc_start: -0.1473 (mmm) cc_final: -0.2273 (mtp) REVERT: f 29 MET cc_start: 0.1745 (ttp) cc_final: 0.1452 (ptm) REVERT: f 219 MET cc_start: 0.9345 (mmp) cc_final: 0.8931 (mmm) REVERT: f 245 MET cc_start: 0.8811 (ptp) cc_final: 0.8593 (ptp) REVERT: f 341 MET cc_start: 0.3618 (tmm) cc_final: 0.3247 (tmm) REVERT: f 396 MET cc_start: 0.9304 (mmp) cc_final: 0.9064 (mmm) REVERT: c 245 MET cc_start: 0.8174 (ptt) cc_final: 0.6885 (ptt) REVERT: b 29 MET cc_start: 0.1538 (ttt) cc_final: 0.1269 (ttt) REVERT: b 72 TYR cc_start: 0.9182 (m-80) cc_final: 0.8835 (m-80) REVERT: b 111 PHE cc_start: 0.9029 (m-80) cc_final: 0.8485 (m-80) REVERT: b 245 MET cc_start: 0.8510 (ptp) cc_final: 0.7995 (ptp) REVERT: a 29 MET cc_start: 0.3522 (ttm) cc_final: 0.3306 (ttm) REVERT: d 21 MET cc_start: -0.4033 (mmm) cc_final: -0.4317 (mtm) REVERT: d 29 MET cc_start: 0.8841 (ttp) cc_final: 0.8364 (ptm) REVERT: d 147 MET cc_start: 0.8618 (mmp) cc_final: 0.7834 (tpt) REVERT: d 390 MET cc_start: 0.8541 (pmm) cc_final: 0.8147 (pmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1208 time to fit residues: 25.3537 Evaluate side-chains 113 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 25 ASN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 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 = 0.3442 r_free = 0.3442 target = 0.033924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.027032 restraints weight = 334263.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.027616 restraints weight = 256552.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.028047 restraints weight = 210448.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.028363 restraints weight = 181367.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.028599 restraints weight = 161675.273| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5203 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= 0.167 Angle : 0.670 9.332 27503 Z= 0.323 Chirality : 0.043 0.382 3135 Planarity : 0.004 0.040 3525 Dihedral : 10.384 162.889 2917 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.67 (0.17), residues: 2490 helix: 0.80 (0.15), residues: 1182 sheet: -0.33 (0.26), residues: 390 loop : 0.61 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 221 TYR 0.013 0.002 TYR d 332 PHE 0.017 0.001 PHE f 412 TRP 0.004 0.001 TRP c 381 HIS 0.011 0.001 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (20371) covalent geometry : angle 0.67043 / 0.32 (27503) hydrogen bonds : bond 0.03118 / 2.38 ( 944) hydrogen bonds : angle 4.34951 / 3.36 ( 2742) Misc. bond : bond 0.00553 / 0.49 ( 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 : 0.667 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: e 1 MET cc_start: 0.8232 (pmm) cc_final: 0.7831 (pmm) REVERT: e 21 MET cc_start: -0.1256 (ttt) cc_final: -0.1500 (ttt) REVERT: e 29 MET cc_start: 0.4793 (ttm) cc_final: 0.4548 (ttm) REVERT: e 327 MET cc_start: 0.9607 (tmm) cc_final: 0.9399 (tmm) REVERT: f 21 MET cc_start: -0.1011 (mmm) cc_final: -0.1832 (mtt) REVERT: f 29 MET cc_start: 0.1532 (ttp) cc_final: 0.1285 (ptm) REVERT: f 219 MET cc_start: 0.9287 (mmp) cc_final: 0.8859 (mmm) REVERT: f 341 MET cc_start: 0.3582 (tmm) cc_final: 0.3217 (tmm) REVERT: f 396 MET cc_start: 0.9158 (mmp) cc_final: 0.8768 (mtp) REVERT: c 205 MET cc_start: 0.8611 (tpt) cc_final: 0.8395 (tpt) REVERT: b 29 MET cc_start: 0.1458 (ttt) cc_final: 0.1214 (ttt) REVERT: b 72 TYR cc_start: 0.9073 (m-80) cc_final: 0.8721 (m-10) REVERT: b 111 PHE cc_start: 0.8928 (m-80) cc_final: 0.8371 (m-80) REVERT: b 245 MET cc_start: 0.8473 (ptp) cc_final: 0.7968 (ptp) REVERT: b 341 MET cc_start: 0.2140 (mmm) cc_final: 0.1896 (mmm) REVERT: a 1 MET cc_start: 0.6874 (pmm) cc_final: 0.6586 (pmm) REVERT: d 21 MET cc_start: -0.3790 (mmm) cc_final: -0.4088 (mtt) REVERT: d 29 MET cc_start: 0.8840 (ttp) cc_final: 0.8391 (ptm) REVERT: d 147 MET cc_start: 0.8603 (mmp) cc_final: 0.7793 (tpt) REVERT: d 186 MET cc_start: 0.9231 (tmm) cc_final: 0.9010 (tmm) REVERT: d 390 MET cc_start: 0.8577 (pmm) cc_final: 0.8200 (pmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1233 time to fit residues: 24.5515 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 : 0.545 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 164 optimal weight: 0.4980 chunk 15 optimal weight: 20.0000 overall best weight: 2.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 239 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 = 0.3434 r_free = 0.3434 target = 0.033729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.026851 restraints weight = 332159.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.027442 restraints weight = 253793.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.027865 restraints weight = 208005.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.028181 restraints weight = 178873.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.028416 restraints weight = 159396.422| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5476 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= 0.148 Angle : 0.661 7.842 27503 Z= 0.318 Chirality : 0.043 0.260 3135 Planarity : 0.004 0.046 3525 Dihedral : 10.363 162.177 2917 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.72 (0.17), residues: 2490 helix: 0.82 (0.15), residues: 1188 sheet: -0.37 (0.26), residues: 390 loop : 0.70 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 366 TYR 0.043 0.002 TYR c 332 PHE 0.014 0.001 PHE f 412 TRP 0.005 0.001 TRP c 381 HIS 0.013 0.001 HIS c 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (20371) covalent geometry : angle 0.66050 / 0.32 (27503) hydrogen bonds : bond 0.03061 / 2.32 ( 944) hydrogen bonds : angle 4.30311 / 3.34 ( 2742) Misc. bond : bond 0.00372 / 0.39 ( 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 123 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.804 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: e 1 MET cc_start: 0.8155 (pmm) cc_final: 0.7754 (pmm) REVERT: e 21 MET cc_start: -0.1209 (ttt) cc_final: -0.1461 (ttt) REVERT: e 29 MET cc_start: 0.4824 (ttm) cc_final: 0.4085 (ttp) REVERT: e 327 MET cc_start: 0.9609 (tmm) cc_final: 0.9407 (tmm) REVERT: f 1 MET cc_start: 0.4661 (pmm) cc_final: 0.4157 (pmm) REVERT: f 21 MET cc_start: -0.1027 (mmm) cc_final: -0.1935 (mtt) REVERT: f 29 MET cc_start: 0.1638 (ttp) cc_final: 0.1392 (ptm) REVERT: f 219 MET cc_start: 0.9263 (mmp) cc_final: 0.8831 (mmm) REVERT: f 341 MET cc_start: 0.3675 (tmm) cc_final: 0.3319 (tmm) REVERT: f 396 MET cc_start: 0.9154 (mmp) cc_final: 0.8917 (mmm) REVERT: c 205 MET cc_start: 0.8524 (tpt) cc_final: 0.8293 (tpt) REVERT: b 29 MET cc_start: 0.1581 (ttt) cc_final: 0.1295 (ttt) REVERT: b 72 TYR cc_start: 0.9096 (m-80) cc_final: 0.8743 (m-10) REVERT: b 111 PHE cc_start: 0.8972 (m-80) cc_final: 0.8433 (m-80) REVERT: b 207 LEU cc_start: 0.9275 (mp) cc_final: 0.9020 (tt) REVERT: b 245 MET cc_start: 0.8487 (ptp) cc_final: 0.7980 (ptp) REVERT: b 341 MET cc_start: 0.2171 (mmm) cc_final: 0.1918 (mmm) REVERT: b 396 MET cc_start: 0.8241 (mtt) cc_final: 0.7739 (ttt) REVERT: a 29 MET cc_start: 0.2439 (ptm) cc_final: 0.1630 (tmm) REVERT: a 341 MET cc_start: 0.2091 (mmm) cc_final: 0.1890 (mmm) REVERT: d 21 MET cc_start: -0.3801 (mmm) cc_final: -0.4047 (mtt) REVERT: d 147 MET cc_start: 0.8481 (mmp) cc_final: 0.7671 (tpt) REVERT: d 186 MET cc_start: 0.9250 (tmm) cc_final: 0.9000 (tmm) REVERT: d 341 MET cc_start: -0.1074 (mmm) cc_final: -0.2066 (tpp) REVERT: d 390 MET cc_start: 0.8556 (pmm) cc_final: 0.8179 (pmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1131 time to fit residues: 23.0106 Evaluate side-chains 114 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 8.9990 chunk 181 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 40 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 163 optimal weight: 0.0970 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 239 HIS ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** 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 = 0.3448 r_free = 0.3448 target = 0.034261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.027361 restraints weight = 328611.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.027968 restraints weight = 247349.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.028404 restraints weight = 201227.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.028721 restraints weight = 172328.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.028963 restraints weight = 153142.239| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20401 Z= 0.109 Angle : 0.627 8.161 27503 Z= 0.298 Chirality : 0.043 0.259 3135 Planarity : 0.003 0.045 3525 Dihedral : 10.293 162.131 2917 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.82 (0.17), residues: 2490 helix: 0.92 (0.15), residues: 1188 sheet: -0.35 (0.26), residues: 390 loop : 0.74 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 173 TYR 0.021 0.001 TYR c 332 PHE 0.019 0.001 PHE f 412 TRP 0.007 0.001 TRP c 381 HIS 0.008 0.001 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (20371) covalent geometry : angle 0.62718 / 0.30 (27503) hydrogen bonds : bond 0.02775 / 2.08 ( 944) hydrogen bonds : angle 4.24135 / 3.31 ( 2742) Misc. bond : bond 0.00354 / 0.36 ( 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 122 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.707 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: e 1 MET cc_start: 0.7911 (pmm) cc_final: 0.7548 (pmm) REVERT: e 29 MET cc_start: 0.4726 (ttm) cc_final: 0.4308 (ttt) REVERT: e 327 MET cc_start: 0.9597 (tmm) cc_final: 0.9392 (tmm) REVERT: f 1 MET cc_start: 0.4658 (pmm) cc_final: 0.4184 (pmm) REVERT: f 21 MET cc_start: -0.1103 (mmm) cc_final: -0.2216 (mtt) REVERT: f 29 MET cc_start: 0.1448 (ttp) cc_final: 0.1228 (ptm) REVERT: f 219 MET cc_start: 0.9207 (mmp) cc_final: 0.8740 (mmp) REVERT: f 341 MET cc_start: 0.3598 (tmm) cc_final: 0.3257 (tmm) REVERT: f 396 MET cc_start: 0.9142 (mmp) cc_final: 0.8909 (mmm) REVERT: c 205 MET cc_start: 0.8563 (tpt) cc_final: 0.8312 (tpt) REVERT: c 390 MET cc_start: 0.8369 (ptt) cc_final: 0.8114 (ptt) REVERT: b 29 MET cc_start: 0.1631 (ttt) cc_final: 0.1340 (ttt) REVERT: b 72 TYR cc_start: 0.9043 (m-80) cc_final: 0.8666 (m-10) REVERT: b 111 PHE cc_start: 0.8993 (m-80) cc_final: 0.8417 (m-80) REVERT: b 147 MET cc_start: 0.7861 (mpp) cc_final: 0.6847 (tpt) REVERT: b 207 LEU cc_start: 0.9233 (mp) cc_final: 0.8985 (tt) REVERT: b 245 MET cc_start: 0.8478 (ptp) cc_final: 0.7979 (ptp) REVERT: a 29 MET cc_start: 0.2284 (ptm) cc_final: 0.1964 (tmm) REVERT: a 396 MET cc_start: 0.8571 (mtt) cc_final: 0.8072 (mmp) REVERT: d 21 MET cc_start: -0.3907 (mmm) cc_final: -0.4108 (mtt) REVERT: d 29 MET cc_start: 0.8730 (ttp) cc_final: 0.8338 (ptm) REVERT: d 147 MET cc_start: 0.8513 (mmp) cc_final: 0.7699 (tpt) REVERT: d 186 MET cc_start: 0.9295 (tmm) cc_final: 0.9025 (tmm) REVERT: d 341 MET cc_start: -0.1092 (mmm) cc_final: -0.1293 (mmm) REVERT: d 390 MET cc_start: 0.8511 (pmm) cc_final: 0.8154 (pmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1096 time to fit residues: 22.1991 Evaluate side-chains 113 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 0.0570 chunk 235 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 overall best weight: 4.8104 ------------------------------------------------------------------------------- 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** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 ASN b 126 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3367 r_free = 0.3367 target = 0.031352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.024705 restraints weight = 348734.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.025249 restraints weight = 268713.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.025642 restraints weight = 221239.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.025932 restraints weight = 191166.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.026149 restraints weight = 171099.803| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 20401 Z= 0.247 Angle : 0.816 10.288 27503 Z= 0.397 Chirality : 0.045 0.228 3135 Planarity : 0.004 0.039 3525 Dihedral : 10.449 159.319 2917 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.40 (0.17), residues: 2490 helix: 0.57 (0.14), residues: 1176 sheet: -0.52 (0.26), residues: 402 loop : 0.51 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 366 TYR 0.020 0.003 TYR c 332 PHE 0.020 0.002 PHE b 111 TRP 0.008 0.002 TRP e 381 HIS 0.010 0.002 HIS c 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 (20371) covalent geometry : angle 0.81597 / 0.40 (27503) hydrogen bonds : bond 0.03753 / 2.92 ( 944) hydrogen bonds : angle 4.54042 / 3.49 ( 2742) Misc. bond : bond 0.00345 / 0.36 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.74 seconds wall clock time: 48 minutes 6.47 seconds (2886.47 seconds total)