Starting phenix.real_space_refine on Fri Aug 7 07:57:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2026/8e5p_27917.map" } resolution = 4.4 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 20 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12524 2.51 5 N 3538 2.21 5 O 3824 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: 20038 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.33, per 1000 atoms: 0.22 Number of scatterers: 20038 At special positions: 0 Unit cell: (139.7, 116.6, 148.5, 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 20 15.00 Mg 6 11.99 F 18 9.00 O 3824 8.00 N 3538 7.00 C 12524 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: 1.89 Conformation dependent library (CDL) restraints added in 788.3 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: 0.62 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 256 removed outlier: 3.594A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) 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: 3.555A 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: 3.554A 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: 3.717A 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: 3.700A 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: 4.269A 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: 4.268A 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: 3.596A 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: 3.599A 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: 3.701A 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: 4.202A 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: 3.721A 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: 4.266A 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: 3.594A 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: 3.554A 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: 4.238A pdb=" N VAL e 119 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.876A 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: 7.222A 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: 3.803A 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: 4.477A 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: 3.632A 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: 7.517A 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: 4.237A 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: 4.133A 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: 3.511A 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: 4.479A 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: 3.632A pdb=" N ALA f 317 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.324A 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: 7.098A 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: 3.851A 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: 6.879A pdb=" N SER c 98 " --> pdb=" O ASN c 117 " (cutoff:3.500A) removed outlier: 4.132A 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: 6.119A 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: 4.478A 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: 3.692A 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: 3.855A 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: 4.136A 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: 4.476A 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: 6.323A 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: 3.693A 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: 3.853A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR a 96 " --> pdb=" O VAL a 119 " (cutoff:3.500A) removed outlier: 4.241A 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: 7.221A 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: 4.477A 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: 3.632A 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: 7.522A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.100A 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: 3.694A 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: 3.853A 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: 4.136A 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: 6.118A 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: 7.096A 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: 3.903A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 364 " --> pdb=" O GLU d 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 944 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.42 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: 4633 1.33 - 1.45: 3721 1.45 - 1.57: 11764 1.57 - 1.69: 33 1.69 - 1.81: 198 Bond restraints: 20349 Sorted by residual: bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.564 -0.088 2.00e-02 2.50e+03 1.93e+01 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 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 1.563 -0.087 2.00e-02 2.50e+03 1.89e+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 1.82e+01 ... (remaining 20344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 27254 2.89 - 5.77: 166 5.77 - 8.66: 37 8.66 - 11.54: 6 11.54 - 14.43: 6 Bond angle restraints: 27469 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 112.58 105.29 7.29 1.22e+00 6.72e-01 3.57e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.74 6.59 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 111.33 105.03 6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " pdb=" F3 BEF e1002 " ideal model delta sigma weight residual 119.96 105.53 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.54 14.42 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 12388 29.83 - 59.65: 147 59.65 - 89.48: 48 89.48 - 119.31: 2 119.31 - 149.14: 6 Dihedral angle restraints: 12591 sinusoidal: 5397 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 89.13 -149.14 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP c1000 " pdb=" O3A ADP c1000 " pdb=" PB ADP c1000 " pdb=" PA ADP c1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.09 -149.10 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 84.35 -144.35 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2606 0.052 - 0.104: 407 0.104 - 0.155: 111 0.155 - 0.207: 5 0.207 - 0.259: 1 Chirality restraints: 3130 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 1.68e+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 8.99e-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 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 3127 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+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 5.66e-02 3.20e+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 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ILE c 331 " -0.086 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 3521 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 55 2.02 - 2.74: 1636 2.74 - 3.46: 29031 3.46 - 4.18: 46224 4.18 - 4.90: 83568 Nonbonded interactions: 160514 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 1.417 3.120 nonbonded pdb=" NZ LYS e 385 " pdb=" O LYS d 352 " model vdw 1.494 3.120 ... (remaining 160509 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: 4.750 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3335 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 20379 Z= 1.844 Angle : 0.642 14.431 27469 Z= 0.353 Chirality : 0.041 0.259 3130 Planarity : 0.004 0.065 3524 Dihedral : 11.506 149.136 7935 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.66 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 0.017 0.001 TYR d 332 PHE 0.007 0.001 PHE b 36 TRP 0.003 0.001 TRP a 381 HIS 0.002 0.000 HIS e 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.21 (20349) covalent geometry : angle 0.64168 / 0.35 (27469) hydrogen bonds : bond 0.19911 / 14.53 ( 944) hydrogen bonds : angle 6.53604 / 5.00 ( 2742) Misc. bond : bond 0.47742 / 50.33 ( 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 198 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.595 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.2762 (mmm) cc_final: 0.1608 (ttt) REVERT: c 29 MET cc_start: -0.3216 (mtp) cc_final: -0.3709 (ttt) REVERT: c 341 MET cc_start: -0.1671 (ttm) cc_final: -0.1952 (tmm) outliers start: 35 outliers final: 9 residues processed: 198 average time/residue: 0.1454 time to fit residues: 45.4305 Evaluate side-chains 126 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 241 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.042641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.034840 restraints weight = 340479.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.035132 restraints weight = 317238.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.035355 restraints weight = 295429.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.035355 restraints weight = 274078.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.035355 restraints weight = 274078.272| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20379 Z= 0.182 Angle : 0.752 9.344 27469 Z= 0.361 Chirality : 0.045 0.256 3130 Planarity : 0.006 0.120 3524 Dihedral : 10.258 167.366 2901 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % 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: 0.01 (0.17), residues: 2490 helix: 0.75 (0.16), residues: 1128 sheet: -1.02 (0.23), residues: 426 loop : -0.21 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG f 212 TYR 0.036 0.002 TYR d 332 PHE 0.027 0.002 PHE b 335 TRP 0.007 0.002 TRP d 381 HIS 0.003 0.001 HIS e 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (20349) covalent geometry : angle 0.75223 / 0.36 (27469) hydrogen bonds : bond 0.03977 / 2.93 ( 944) hydrogen bonds : angle 4.91101 / 3.74 ( 2742) Misc. bond : bond 0.00583 / 0.67 ( 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 118 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.578 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: f 21 MET cc_start: 0.0664 (mmm) cc_final: 0.0118 (mtt) REVERT: f 29 MET cc_start: 0.2151 (mtp) cc_final: 0.1151 (ttm) REVERT: f 147 MET cc_start: 0.8407 (mmp) cc_final: 0.7652 (mpp) REVERT: f 219 MET cc_start: 0.9390 (mmp) cc_final: 0.9059 (mmt) REVERT: f 380 MET cc_start: 0.9117 (tmm) cc_final: 0.8894 (tmm) REVERT: f 396 MET cc_start: 0.9234 (mmp) cc_final: 0.8989 (mmp) REVERT: c 21 MET cc_start: 0.5970 (mmm) cc_final: 0.5609 (ptm) REVERT: c 29 MET cc_start: -0.0412 (mtp) cc_final: -0.0980 (ttt) REVERT: c 341 MET cc_start: -0.2419 (ttm) cc_final: -0.3101 (tmm) REVERT: c 405 MET cc_start: 0.8835 (ptp) cc_final: 0.8499 (ppp) REVERT: b 147 MET cc_start: 0.7804 (mmm) cc_final: 0.7482 (mpp) REVERT: b 396 MET cc_start: 0.7623 (mtp) cc_final: 0.6944 (mtp) REVERT: a 219 MET cc_start: 0.9247 (mmp) cc_final: 0.8765 (mmm) REVERT: a 380 MET cc_start: 0.9441 (mmp) cc_final: 0.9221 (mmm) REVERT: a 390 MET cc_start: 0.7349 (pmm) cc_final: 0.6576 (pmm) REVERT: a 396 MET cc_start: 0.9173 (mtp) cc_final: 0.8952 (mtp) REVERT: d 21 MET cc_start: 0.3110 (mmp) cc_final: 0.1835 (ptm) REVERT: d 396 MET cc_start: 0.9127 (mtp) cc_final: 0.8796 (mtp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1281 time to fit residues: 24.7575 Evaluate side-chains 111 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 176 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 172 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 ASN ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 HIS a 135 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.039323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.031869 restraints weight = 353310.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.032103 restraints weight = 324659.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.032229 restraints weight = 304384.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.032406 restraints weight = 291649.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.032505 restraints weight = 279669.494| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 20379 Z= 0.226 Angle : 0.776 9.151 27469 Z= 0.378 Chirality : 0.044 0.186 3130 Planarity : 0.005 0.055 3524 Dihedral : 10.159 161.262 2901 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.29 % 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: 0.33 (0.17), residues: 2490 helix: 0.58 (0.15), residues: 1170 sheet: -0.28 (0.25), residues: 414 loop : 0.25 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 173 TYR 0.019 0.002 TYR e 332 PHE 0.034 0.002 PHE e 413 TRP 0.006 0.001 TRP f 381 HIS 0.006 0.002 HIS c 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (20349) covalent geometry : angle 0.77574 / 0.38 (27469) hydrogen bonds : bond 0.03897 / 2.90 ( 944) hydrogen bonds : angle 4.44360 / 3.38 ( 2742) Misc. bond : bond 0.00398 / 0.40 ( 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 113 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.743 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: e 29 MET cc_start: 0.2993 (ttt) cc_final: 0.2611 (ttt) REVERT: e 390 MET cc_start: 0.8089 (pmm) cc_final: 0.7842 (pmm) REVERT: f 21 MET cc_start: 0.1467 (mmm) cc_final: 0.0914 (mtt) REVERT: f 29 MET cc_start: 0.2259 (mtp) cc_final: 0.1293 (ttm) REVERT: f 147 MET cc_start: 0.8401 (mmp) cc_final: 0.7626 (mpp) REVERT: f 219 MET cc_start: 0.9340 (mmp) cc_final: 0.9135 (mmp) REVERT: f 380 MET cc_start: 0.9184 (tmm) cc_final: 0.8983 (tmm) REVERT: f 396 MET cc_start: 0.9354 (mmp) cc_final: 0.9045 (mmp) REVERT: f 405 MET cc_start: 0.9327 (ptp) cc_final: 0.9090 (ppp) REVERT: f 416 MET cc_start: 0.7549 (ppp) cc_final: 0.7300 (ppp) REVERT: c 21 MET cc_start: 0.5940 (mmm) cc_final: 0.5486 (ttp) REVERT: c 29 MET cc_start: 0.0623 (mtp) cc_final: 0.0168 (ttt) REVERT: c 147 MET cc_start: 0.7197 (tpt) cc_final: 0.5432 (mpp) REVERT: c 341 MET cc_start: -0.1166 (ttm) cc_final: -0.2296 (tmm) REVERT: b 147 MET cc_start: 0.7393 (mmm) cc_final: 0.7029 (mpp) REVERT: b 205 MET cc_start: 0.8566 (tpt) cc_final: 0.8160 (tpt) REVERT: b 248 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9140 (mm-30) REVERT: b 390 MET cc_start: 0.4088 (ptt) cc_final: 0.3365 (ptt) REVERT: b 396 MET cc_start: 0.8222 (mtp) cc_final: 0.7522 (mtp) REVERT: a 219 MET cc_start: 0.9354 (mmp) cc_final: 0.8884 (mmm) REVERT: a 390 MET cc_start: 0.7649 (pmm) cc_final: 0.6909 (pmm) REVERT: a 396 MET cc_start: 0.9296 (mmm) cc_final: 0.8797 (ttm) REVERT: d 29 MET cc_start: 0.1281 (ttt) cc_final: 0.0842 (ttt) REVERT: d 147 MET cc_start: 0.9426 (tpp) cc_final: 0.8992 (tpt) REVERT: d 390 MET cc_start: 0.6767 (ptp) cc_final: 0.6076 (ptt) REVERT: d 396 MET cc_start: 0.9346 (mtp) cc_final: 0.8996 (mtp) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.1308 time to fit residues: 24.1936 Evaluate side-chains 104 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 187 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 32 GLN e 172 GLN f 25 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 340 ASN b 25 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.038801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.031420 restraints weight = 356281.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.031594 restraints weight = 327723.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.031831 restraints weight = 308038.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.031885 restraints weight = 292679.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.031885 restraints weight = 285425.365| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20379 Z= 0.157 Angle : 0.650 8.452 27469 Z= 0.314 Chirality : 0.042 0.141 3130 Planarity : 0.004 0.047 3524 Dihedral : 10.073 165.325 2901 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.05 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2490 helix: 0.83 (0.15), residues: 1164 sheet: -0.24 (0.26), residues: 408 loop : 0.38 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 366 TYR 0.017 0.001 TYR d 72 PHE 0.013 0.001 PHE f 355 TRP 0.005 0.001 TRP e 381 HIS 0.004 0.001 HIS f 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (20349) covalent geometry : angle 0.65046 / 0.31 (27469) hydrogen bonds : bond 0.03051 / 2.24 ( 944) hydrogen bonds : angle 4.19814 / 3.22 ( 2742) Misc. bond : bond 0.00210 / 0.22 ( 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 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 MET cc_start: 0.3127 (ttt) cc_final: 0.2584 (ttt) REVERT: e 390 MET cc_start: 0.8188 (pmm) cc_final: 0.7585 (pmm) REVERT: f 21 MET cc_start: 0.1345 (mmm) cc_final: 0.0797 (mtt) REVERT: f 29 MET cc_start: 0.2161 (mtp) cc_final: 0.1434 (ttm) REVERT: f 147 MET cc_start: 0.8179 (mmp) cc_final: 0.7405 (mpp) REVERT: f 219 MET cc_start: 0.9299 (mmp) cc_final: 0.9090 (mmp) REVERT: f 380 MET cc_start: 0.9222 (tmm) cc_final: 0.9012 (tmm) REVERT: f 390 MET cc_start: 0.8324 (ptt) cc_final: 0.7430 (ptt) REVERT: f 396 MET cc_start: 0.9343 (mmp) cc_final: 0.9027 (mmp) REVERT: c 21 MET cc_start: 0.6192 (mmm) cc_final: 0.5690 (ttp) REVERT: c 147 MET cc_start: 0.7086 (tpt) cc_final: 0.5959 (mpp) REVERT: c 341 MET cc_start: -0.1368 (ttm) cc_final: -0.2240 (tmm) REVERT: b 29 MET cc_start: 0.3540 (ttp) cc_final: 0.3141 (ptm) REVERT: b 147 MET cc_start: 0.7578 (mmm) cc_final: 0.6935 (mpp) REVERT: b 205 MET cc_start: 0.8604 (tpt) cc_final: 0.8293 (tpt) REVERT: b 390 MET cc_start: 0.4507 (ptt) cc_final: 0.3827 (ptt) REVERT: a 219 MET cc_start: 0.9251 (mmp) cc_final: 0.8772 (mmm) REVERT: a 380 MET cc_start: 0.9437 (mmp) cc_final: 0.9222 (mmm) REVERT: a 390 MET cc_start: 0.6899 (pmm) cc_final: 0.6476 (pmm) REVERT: d 390 MET cc_start: 0.6742 (ptp) cc_final: 0.5985 (ptt) REVERT: d 396 MET cc_start: 0.9372 (mtp) cc_final: 0.9068 (mtp) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.1424 time to fit residues: 24.9452 Evaluate side-chains 102 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 3 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 219 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 241 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 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 = 0.3675 r_free = 0.3675 target = 0.037540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.030199 restraints weight = 354558.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.030474 restraints weight = 332112.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.030633 restraints weight = 307778.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.030774 restraints weight = 291341.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.030896 restraints weight = 278917.796| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20379 Z= 0.162 Angle : 0.647 8.577 27469 Z= 0.314 Chirality : 0.042 0.148 3130 Planarity : 0.004 0.037 3524 Dihedral : 9.973 163.117 2901 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.05 % Allowed : 1.54 % Favored : 98.41 % 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: 0.86 (0.15), residues: 1170 sheet: -0.26 (0.26), residues: 408 loop : 0.53 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 102 TYR 0.021 0.002 TYR f 332 PHE 0.014 0.001 PHE f 89 TRP 0.003 0.001 TRP e 381 HIS 0.006 0.001 HIS b 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (20349) covalent geometry : angle 0.64714 / 0.31 (27469) hydrogen bonds : bond 0.03086 / 2.28 ( 944) hydrogen bonds : angle 4.12798 / 3.15 ( 2742) Misc. bond : bond 0.00253 / 0.24 ( 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 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 MET cc_start: 0.2747 (ttt) cc_final: 0.1785 (ttt) REVERT: e 390 MET cc_start: 0.8226 (pmm) cc_final: 0.7567 (pmm) REVERT: f 21 MET cc_start: 0.1502 (mmm) cc_final: 0.0959 (mtt) REVERT: f 29 MET cc_start: 0.1507 (mtp) cc_final: 0.0592 (ttp) REVERT: f 219 MET cc_start: 0.9262 (mmp) cc_final: 0.9004 (mmp) REVERT: f 396 MET cc_start: 0.9316 (mmp) cc_final: 0.8966 (mmp) REVERT: c 147 MET cc_start: 0.7233 (tpt) cc_final: 0.6193 (mpp) REVERT: c 341 MET cc_start: -0.1167 (ttm) cc_final: -0.1859 (tmm) REVERT: c 390 MET cc_start: 0.4241 (ptp) cc_final: 0.3762 (pmm) REVERT: b 21 MET cc_start: 0.4088 (ttt) cc_final: 0.3177 (ttt) REVERT: b 147 MET cc_start: 0.7291 (mmm) cc_final: 0.6559 (mpp) REVERT: b 205 MET cc_start: 0.8527 (tpt) cc_final: 0.8302 (tpt) REVERT: b 245 MET cc_start: 0.8606 (ptp) cc_final: 0.8301 (ptt) REVERT: b 248 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9173 (mm-30) REVERT: b 390 MET cc_start: 0.4418 (ptt) cc_final: 0.3646 (ptt) REVERT: b 396 MET cc_start: 0.8348 (mtp) cc_final: 0.7823 (mtp) REVERT: a 219 MET cc_start: 0.9250 (mmp) cc_final: 0.8798 (mmm) REVERT: a 390 MET cc_start: 0.6962 (pmm) cc_final: 0.6614 (pmm) REVERT: d 147 MET cc_start: 0.8198 (tpt) cc_final: 0.7565 (tpt) REVERT: d 341 MET cc_start: -0.2306 (mmt) cc_final: -0.2826 (mmp) REVERT: d 390 MET cc_start: 0.6852 (ptp) cc_final: 0.6045 (ptt) REVERT: d 396 MET cc_start: 0.9351 (mtp) cc_final: 0.8739 (mtp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1365 time to fit residues: 23.9253 Evaluate side-chains 105 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 203 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 42 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.035832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.028795 restraints weight = 363039.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.029098 restraints weight = 335176.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.029250 restraints weight = 307481.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.029378 restraints weight = 290617.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.029526 restraints weight = 281207.833| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20379 Z= 0.206 Angle : 0.730 9.914 27469 Z= 0.355 Chirality : 0.043 0.258 3130 Planarity : 0.004 0.053 3524 Dihedral : 10.078 166.644 2901 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 0.57 (0.17), residues: 2490 helix: 0.79 (0.15), residues: 1170 sheet: -0.32 (0.26), residues: 402 loop : 0.41 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG a 366 TYR 0.039 0.002 TYR b 332 PHE 0.011 0.002 PHE b 50 TRP 0.004 0.001 TRP f 381 HIS 0.011 0.002 HIS b 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (20349) covalent geometry : angle 0.73046 / 0.35 (27469) hydrogen bonds : bond 0.03429 / 2.58 ( 944) hydrogen bonds : angle 4.19105 / 3.24 ( 2742) Misc. bond : bond 0.00721 / 0.74 ( 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 105 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.559 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: e 29 MET cc_start: 0.2801 (ttt) cc_final: 0.1956 (ttt) REVERT: e 341 MET cc_start: -0.2206 (mpp) cc_final: -0.2421 (mpp) REVERT: e 390 MET cc_start: 0.8278 (pmm) cc_final: 0.7617 (pmm) REVERT: f 21 MET cc_start: 0.1831 (mmm) cc_final: 0.1126 (mtt) REVERT: f 29 MET cc_start: 0.1912 (mtp) cc_final: 0.1411 (ttm) REVERT: f 219 MET cc_start: 0.9307 (mmp) cc_final: 0.9057 (mmp) REVERT: f 396 MET cc_start: 0.9358 (mmp) cc_final: 0.9060 (mmp) REVERT: c 147 MET cc_start: 0.7204 (tpt) cc_final: 0.6383 (mpp) REVERT: c 341 MET cc_start: -0.0903 (ttm) cc_final: -0.1758 (tmm) REVERT: b 21 MET cc_start: 0.4120 (ttt) cc_final: 0.3272 (ttt) REVERT: b 29 MET cc_start: 0.3747 (ttp) cc_final: 0.3467 (ptm) REVERT: b 147 MET cc_start: 0.7585 (mmm) cc_final: 0.6610 (mpp) REVERT: b 205 MET cc_start: 0.8565 (tpt) cc_final: 0.8351 (tpt) REVERT: b 327 MET cc_start: 0.8722 (ttp) cc_final: 0.8510 (tmm) REVERT: b 390 MET cc_start: 0.5206 (ptt) cc_final: 0.4729 (ptt) REVERT: b 396 MET cc_start: 0.8308 (mtp) cc_final: 0.7653 (mtp) REVERT: a 219 MET cc_start: 0.9270 (mmp) cc_final: 0.8846 (mmm) REVERT: a 390 MET cc_start: 0.7070 (pmm) cc_final: 0.6732 (pmm) REVERT: d 147 MET cc_start: 0.8243 (tpt) cc_final: 0.7554 (tpt) REVERT: d 390 MET cc_start: 0.6879 (ptp) cc_final: 0.6101 (ptt) REVERT: d 396 MET cc_start: 0.9331 (mtp) cc_final: 0.8954 (mtp) REVERT: d 416 MET cc_start: 0.5717 (ptt) cc_final: 0.5098 (ptt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1276 time to fit residues: 22.0165 Evaluate side-chains 100 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 239 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** 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 = 0.3635 r_free = 0.3635 target = 0.036275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.029231 restraints weight = 360538.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.029534 restraints weight = 329378.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.029715 restraints weight = 303773.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.029856 restraints weight = 284098.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.030004 restraints weight = 273432.598| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20379 Z= 0.109 Angle : 0.604 9.021 27469 Z= 0.288 Chirality : 0.043 0.228 3130 Planarity : 0.004 0.052 3524 Dihedral : 9.981 163.926 2901 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.03 (0.15), residues: 1170 sheet: -0.29 (0.26), residues: 390 loop : 0.46 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 252 TYR 0.018 0.001 TYR a 332 PHE 0.010 0.001 PHE a 398 TRP 0.004 0.001 TRP e 381 HIS 0.012 0.001 HIS b 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (20349) covalent geometry : angle 0.60363 / 0.29 (27469) hydrogen bonds : bond 0.02783 / 2.07 ( 944) hydrogen bonds : angle 4.02715 / 3.11 ( 2742) Misc. bond : bond 0.00267 / 0.28 ( 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 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.779 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: e 29 MET cc_start: 0.3234 (ttt) cc_final: 0.2366 (ttt) REVERT: e 390 MET cc_start: 0.8305 (pmm) cc_final: 0.7665 (pmm) REVERT: f 21 MET cc_start: 0.1718 (mmm) cc_final: 0.1139 (mtt) REVERT: f 29 MET cc_start: 0.1707 (mtp) cc_final: 0.0743 (ttp) REVERT: f 147 MET cc_start: 0.8240 (mmp) cc_final: 0.7252 (mpp) REVERT: f 219 MET cc_start: 0.9172 (mmp) cc_final: 0.8935 (mmp) REVERT: f 396 MET cc_start: 0.9304 (mmp) cc_final: 0.8956 (mmp) REVERT: c 341 MET cc_start: -0.0972 (ttm) cc_final: -0.1878 (tmm) REVERT: c 390 MET cc_start: 0.4490 (ptp) cc_final: 0.4134 (pmm) REVERT: b 21 MET cc_start: 0.4006 (ttt) cc_final: 0.3147 (ttt) REVERT: b 29 MET cc_start: 0.3278 (ttp) cc_final: 0.3066 (ptm) REVERT: b 147 MET cc_start: 0.7482 (mmm) cc_final: 0.6560 (mpp) REVERT: b 205 MET cc_start: 0.8572 (tpt) cc_final: 0.8336 (tpt) REVERT: b 390 MET cc_start: 0.5038 (ptt) cc_final: 0.4138 (ptt) REVERT: b 396 MET cc_start: 0.8453 (mtp) cc_final: 0.7973 (mtp) REVERT: a 1 MET cc_start: 0.7844 (pmm) cc_final: 0.7407 (pmm) REVERT: a 219 MET cc_start: 0.9170 (mmp) cc_final: 0.8753 (mmm) REVERT: a 390 MET cc_start: 0.7015 (pmm) cc_final: 0.6528 (pmm) REVERT: d 341 MET cc_start: -0.2433 (mmt) cc_final: -0.2699 (mmp) REVERT: d 390 MET cc_start: 0.7022 (ptp) cc_final: 0.6170 (ptt) REVERT: d 396 MET cc_start: 0.9319 (mtp) cc_final: 0.8936 (mtp) REVERT: d 416 MET cc_start: 0.5538 (ptt) cc_final: 0.4913 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1361 time to fit residues: 23.7580 Evaluate side-chains 99 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 138 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 232 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 126 ASN ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 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 = 0.3612 r_free = 0.3612 target = 0.035457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.028465 restraints weight = 368213.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.028755 restraints weight = 335803.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.028966 restraints weight = 308163.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.029108 restraints weight = 289245.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.029173 restraints weight = 276698.181| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20379 Z= 0.152 Angle : 0.646 7.547 27469 Z= 0.312 Chirality : 0.042 0.170 3130 Planarity : 0.004 0.066 3524 Dihedral : 9.909 162.055 2901 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.77 (0.17), residues: 2490 helix: 1.03 (0.15), residues: 1170 sheet: -0.33 (0.26), residues: 390 loop : 0.45 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG a 173 TYR 0.012 0.001 TYR b 332 PHE 0.012 0.001 PHE a 89 TRP 0.002 0.001 TRP e 381 HIS 0.010 0.001 HIS b 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (20349) covalent geometry : angle 0.64554 / 0.31 (27469) hydrogen bonds : bond 0.02969 / 2.25 ( 944) hydrogen bonds : angle 4.10000 / 3.18 ( 2742) Misc. bond : bond 0.00317 / 0.31 ( 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 102 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.547 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: e 341 MET cc_start: -0.2262 (mpp) cc_final: -0.2906 (mmt) REVERT: e 390 MET cc_start: 0.8412 (pmm) cc_final: 0.7799 (pmm) REVERT: f 21 MET cc_start: 0.1787 (mmm) cc_final: 0.1075 (mtt) REVERT: f 29 MET cc_start: 0.1815 (mtp) cc_final: 0.1052 (ttp) REVERT: f 147 MET cc_start: 0.8301 (mmp) cc_final: 0.7256 (mpp) REVERT: f 396 MET cc_start: 0.9321 (mmp) cc_final: 0.8768 (mtp) REVERT: c 341 MET cc_start: -0.0670 (ttm) cc_final: -0.1647 (tmm) REVERT: b 21 MET cc_start: 0.4125 (ttt) cc_final: 0.3221 (ttt) REVERT: b 29 MET cc_start: 0.3580 (ttp) cc_final: 0.3311 (ptm) REVERT: b 147 MET cc_start: 0.7589 (mmm) cc_final: 0.6570 (mpp) REVERT: b 205 MET cc_start: 0.8598 (tpt) cc_final: 0.8300 (tpt) REVERT: b 245 MET cc_start: 0.8806 (ptp) cc_final: 0.8583 (ptt) REVERT: b 390 MET cc_start: 0.5137 (ptt) cc_final: 0.4367 (ptt) REVERT: b 396 MET cc_start: 0.8399 (mtp) cc_final: 0.7705 (mtp) REVERT: a 1 MET cc_start: 0.7620 (pmm) cc_final: 0.7190 (pmm) REVERT: a 219 MET cc_start: 0.9170 (mmp) cc_final: 0.8779 (mmm) REVERT: a 390 MET cc_start: 0.7095 (pmm) cc_final: 0.6641 (pmm) REVERT: d 341 MET cc_start: -0.1953 (mmt) cc_final: -0.2337 (mmp) REVERT: d 390 MET cc_start: 0.6923 (ptp) cc_final: 0.6122 (ptt) REVERT: d 396 MET cc_start: 0.9371 (mtp) cc_final: 0.9003 (mtp) REVERT: d 416 MET cc_start: 0.5607 (ptt) cc_final: 0.5399 (ptt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1196 time to fit residues: 20.5207 Evaluate side-chains 99 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** 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 = 0.3615 r_free = 0.3615 target = 0.035570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.028689 restraints weight = 362557.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.028893 restraints weight = 328175.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.029120 restraints weight = 304436.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.029215 restraints weight = 286445.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.029363 restraints weight = 275745.514| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20379 Z= 0.105 Angle : 0.603 10.013 27469 Z= 0.289 Chirality : 0.042 0.195 3130 Planarity : 0.004 0.076 3524 Dihedral : 9.849 163.037 2901 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.87 (0.17), residues: 2490 helix: 1.09 (0.15), residues: 1170 sheet: -0.30 (0.26), residues: 390 loop : 0.54 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 173 TYR 0.013 0.001 TYR b 332 PHE 0.010 0.001 PHE d 355 TRP 0.004 0.001 TRP e 381 HIS 0.012 0.001 HIS f 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20349) covalent geometry : angle 0.60332 / 0.29 (27469) hydrogen bonds : bond 0.02663 / 2.00 ( 944) hydrogen bonds : angle 4.03546 / 3.13 ( 2742) Misc. bond : bond 0.00319 / 0.32 ( 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 102 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.491 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: e 21 MET cc_start: -0.0509 (ttt) cc_final: -0.0741 (ttt) REVERT: e 29 MET cc_start: 0.3507 (ttt) cc_final: 0.2771 (ttt) REVERT: e 341 MET cc_start: -0.2268 (mpp) cc_final: -0.2645 (mmt) REVERT: e 390 MET cc_start: 0.8391 (pmm) cc_final: 0.7754 (pmm) REVERT: f 21 MET cc_start: 0.1767 (mmm) cc_final: 0.0993 (mtt) REVERT: f 29 MET cc_start: 0.1638 (mtp) cc_final: 0.0879 (ttp) REVERT: f 396 MET cc_start: 0.9327 (mmp) cc_final: 0.8977 (mmp) REVERT: c 1 MET cc_start: 0.6405 (ptt) cc_final: 0.5572 (ppp) REVERT: c 341 MET cc_start: -0.0818 (ttm) cc_final: -0.1768 (tmm) REVERT: c 390 MET cc_start: 0.4744 (ptp) cc_final: 0.4300 (pmm) REVERT: b 21 MET cc_start: 0.4141 (ttt) cc_final: 0.3397 (ttt) REVERT: b 29 MET cc_start: 0.3377 (ttp) cc_final: 0.3086 (ptm) REVERT: b 147 MET cc_start: 0.7609 (mmm) cc_final: 0.6579 (mpp) REVERT: b 205 MET cc_start: 0.8620 (tpt) cc_final: 0.8362 (tpt) REVERT: b 390 MET cc_start: 0.5128 (ptt) cc_final: 0.4181 (ptt) REVERT: b 396 MET cc_start: 0.8422 (mtp) cc_final: 0.7763 (mtp) REVERT: a 219 MET cc_start: 0.9096 (mmp) cc_final: 0.8695 (mmm) REVERT: a 390 MET cc_start: 0.6980 (pmm) cc_final: 0.6756 (pmm) REVERT: a 396 MET cc_start: 0.9270 (ttt) cc_final: 0.8989 (ppp) REVERT: d 341 MET cc_start: -0.2193 (mmt) cc_final: -0.2541 (mmp) REVERT: d 390 MET cc_start: 0.6907 (ptp) cc_final: 0.6038 (ptt) REVERT: d 396 MET cc_start: 0.9330 (mtp) cc_final: 0.8935 (mtp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1224 time to fit residues: 20.8628 Evaluate side-chains 99 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 105 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 126 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 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 = 0.3571 r_free = 0.3571 target = 0.034171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.027399 restraints weight = 371514.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.027654 restraints weight = 334766.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.027871 restraints weight = 308475.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.028051 restraints weight = 277548.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.028328 restraints weight = 255624.864| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20379 Z= 0.184 Angle : 0.692 9.363 27469 Z= 0.337 Chirality : 0.043 0.192 3130 Planarity : 0.004 0.054 3524 Dihedral : 9.881 161.771 2901 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 0.70 (0.17), residues: 2490 helix: 0.96 (0.15), residues: 1170 sheet: -0.39 (0.26), residues: 390 loop : 0.45 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 173 TYR 0.015 0.002 TYR f 72 PHE 0.020 0.002 PHE f 121 TRP 0.005 0.001 TRP f 381 HIS 0.008 0.002 HIS b 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (20349) covalent geometry : angle 0.69234 / 0.34 (27469) hydrogen bonds : bond 0.03245 / 2.49 ( 944) hydrogen bonds : angle 4.17774 / 3.23 ( 2742) Misc. bond : bond 0.00333 / 0.33 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.912 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: e 1 MET cc_start: 0.6406 (pmm) cc_final: 0.5786 (ptp) REVERT: e 21 MET cc_start: -0.0247 (ttt) cc_final: -0.0502 (ttt) REVERT: e 341 MET cc_start: -0.1935 (mpp) cc_final: -0.2408 (mmt) REVERT: e 390 MET cc_start: 0.8456 (pmm) cc_final: 0.7870 (pmm) REVERT: f 21 MET cc_start: 0.2382 (mmm) cc_final: 0.1682 (mtt) REVERT: f 29 MET cc_start: 0.2170 (mtp) cc_final: 0.1544 (ttp) REVERT: f 147 MET cc_start: 0.8447 (mmp) cc_final: 0.7251 (mpp) REVERT: f 219 MET cc_start: 0.9375 (mmp) cc_final: 0.9152 (mmm) REVERT: f 396 MET cc_start: 0.9327 (mmp) cc_final: 0.8993 (mmp) REVERT: c 1 MET cc_start: 0.6837 (ptt) cc_final: 0.6480 (ptt) REVERT: c 341 MET cc_start: -0.0371 (ttm) cc_final: -0.1356 (tmm) REVERT: b 21 MET cc_start: 0.4289 (ttt) cc_final: 0.3386 (ttt) REVERT: b 29 MET cc_start: 0.3687 (ttp) cc_final: 0.3375 (ptm) REVERT: b 205 MET cc_start: 0.8710 (tpt) cc_final: 0.8414 (tpt) REVERT: b 390 MET cc_start: 0.5809 (ptt) cc_final: 0.5107 (ptt) REVERT: b 396 MET cc_start: 0.8581 (mtp) cc_final: 0.7913 (mtp) REVERT: a 147 MET cc_start: 0.6965 (tpt) cc_final: 0.6372 (mpp) REVERT: a 219 MET cc_start: 0.9293 (mmp) cc_final: 0.8963 (mmm) REVERT: a 390 MET cc_start: 0.7400 (pmm) cc_final: 0.7146 (pmm) REVERT: a 396 MET cc_start: 0.9214 (ttt) cc_final: 0.8925 (ppp) REVERT: d 29 MET cc_start: 0.2402 (ptm) cc_final: 0.1994 (tmm) REVERT: d 341 MET cc_start: -0.1486 (mmt) cc_final: -0.1706 (mmp) REVERT: d 390 MET cc_start: 0.6884 (ptp) cc_final: 0.6052 (ptt) REVERT: d 396 MET cc_start: 0.9319 (mtp) cc_final: 0.8948 (mtp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1358 time to fit residues: 24.1364 Evaluate side-chains 100 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 209 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 62 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 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 = 0.3578 r_free = 0.3578 target = 0.034392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.027606 restraints weight = 369661.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.027831 restraints weight = 332352.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.027991 restraints weight = 308850.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.028156 restraints weight = 294022.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.028293 restraints weight = 278411.615| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20379 Z= 0.113 Angle : 0.609 7.381 27469 Z= 0.293 Chirality : 0.042 0.168 3130 Planarity : 0.003 0.053 3524 Dihedral : 9.796 162.916 2901 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2490 helix: 1.07 (0.15), residues: 1170 sheet: -0.27 (0.26), residues: 384 loop : 0.51 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 173 TYR 0.021 0.001 TYR c 72 PHE 0.017 0.001 PHE f 121 TRP 0.003 0.001 TRP e 381 HIS 0.006 0.001 HIS b 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (20349) covalent geometry : angle 0.60886 / 0.29 (27469) hydrogen bonds : bond 0.02679 / 2.04 ( 944) hydrogen bonds : angle 4.03890 / 3.13 ( 2742) Misc. bond : bond 0.00290 / 0.29 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.39 seconds wall clock time: 59 minutes 4.73 seconds (3544.73 seconds total)