Starting phenix.real_space_refine on Sun Aug 24 13:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_27917_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_27917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_27917.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_27917_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5p_27917/08_2025/8e5p_27917_neut.cif" } 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-2.0-5787/lib/python3.9/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: 5.65, per 1000 atoms: 0.28 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.97 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: 4.07 Time building geometry restraints manager: 2.78 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: 2607 0.052 - 0.104: 406 0.104 - 0.155: 109 0.155 - 0.207: 7 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.000 Find NCS groups from input model: 0.410 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3583 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 : 0.641 14.431 27469 Z= 0.351 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 aren 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 covalent geometry : bond 0.00344 (20349) covalent geometry : angle 0.64136 (27469) hydrogen bonds : bond 0.19911 ( 944) hydrogen bonds : angle 6.53604 ( 2742) Misc. bond : bond 0.47742 ( 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 : 0.871 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: 0.1589 time to fit residues: 49.0043 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 : 0.845 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: e 172 GLN e 241 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.041740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.034041 restraints weight = 344083.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.034369 restraints weight = 317305.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.034564 restraints weight = 293709.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.034697 restraints weight = 278500.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.034769 restraints weight = 267640.170| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20379 Z= 0.160 Angle : 0.703 8.732 27469 Z= 0.337 Chirality : 0.044 0.186 3130 Planarity : 0.005 0.099 3524 Dihedral : 10.324 164.042 2901 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.17 % Favored : 97.79 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.79 % 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 aren not related in a simple way. whole: 0.09 (0.17), residues: 2490 helix: 0.75 (0.16), residues: 1128 sheet: -0.91 (0.24), residues: 426 loop : -0.11 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG f 212 TYR 0.027 0.002 TYR d 332 PHE 0.035 0.002 PHE b 335 TRP 0.005 0.001 TRP d 381 HIS 0.007 0.001 HIS a 388 Details of bonding type rmsd covalent geometry : bond 0.00340 (20349) covalent geometry : angle 0.70278 (27469) hydrogen bonds : bond 0.03448 ( 944) hydrogen bonds : angle 4.60850 ( 2742) Misc. bond : bond 0.00408 ( 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 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.602 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: 0.3746 (mtp) cc_final: 0.3540 (ttm) REVERT: e 380 MET cc_start: 0.9507 (mmm) cc_final: 0.9270 (mmm) REVERT: f 21 MET cc_start: 0.0785 (mmm) cc_final: 0.0234 (mtt) REVERT: f 29 MET cc_start: 0.1973 (mtp) cc_final: 0.0973 (ttm) REVERT: f 147 MET cc_start: 0.8367 (mmp) cc_final: 0.7620 (mpp) REVERT: f 219 MET cc_start: 0.9217 (mmp) cc_final: 0.8982 (mmp) REVERT: f 248 GLU cc_start: 0.9298 (mp0) cc_final: 0.9083 (mm-30) REVERT: f 380 MET cc_start: 0.9233 (tmm) cc_final: 0.8998 (tmm) REVERT: f 396 MET cc_start: 0.9239 (mmp) cc_final: 0.8988 (mmp) REVERT: c 21 MET cc_start: 0.5958 (mmm) cc_final: 0.5532 (ptm) REVERT: c 29 MET cc_start: -0.0749 (mtp) cc_final: -0.1135 (ttt) REVERT: c 341 MET cc_start: -0.1999 (ttm) cc_final: -0.2717 (tmm) REVERT: c 405 MET cc_start: 0.8940 (ptp) cc_final: 0.8500 (ppp) REVERT: b 29 MET cc_start: 0.2012 (ttm) cc_final: 0.1705 (ttt) REVERT: b 390 MET cc_start: 0.4504 (ptm) cc_final: 0.4286 (ptt) REVERT: b 396 MET cc_start: 0.7898 (mtp) cc_final: 0.7325 (mtp) REVERT: a 219 MET cc_start: 0.9243 (mmp) cc_final: 0.8750 (mmm) REVERT: a 380 MET cc_start: 0.9411 (mmp) cc_final: 0.9167 (mmm) REVERT: a 390 MET cc_start: 0.7414 (pmm) cc_final: 0.6730 (pmm) REVERT: a 396 MET cc_start: 0.9187 (mtp) cc_final: 0.8055 (ttm) REVERT: d 147 MET cc_start: 0.9432 (tpp) cc_final: 0.9222 (tpp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1242 time to fit residues: 24.0599 Evaluate side-chains 110 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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: 8.9990 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.040529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.032930 restraints weight = 346453.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.033216 restraints weight = 320832.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.033428 restraints weight = 298138.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.033428 restraints weight = 277289.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.033428 restraints weight = 277288.431| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20379 Z= 0.122 Angle : 0.598 7.927 27469 Z= 0.286 Chirality : 0.041 0.141 3130 Planarity : 0.004 0.036 3524 Dihedral : 9.938 161.744 2901 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2490 helix: 0.95 (0.15), residues: 1158 sheet: -0.54 (0.25), residues: 408 loop : 0.30 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 173 TYR 0.015 0.001 TYR d 332 PHE 0.010 0.001 PHE b 335 TRP 0.003 0.001 TRP e 381 HIS 0.004 0.001 HIS a 344 Details of bonding type rmsd covalent geometry : bond 0.00253 (20349) covalent geometry : angle 0.59754 (27469) hydrogen bonds : bond 0.02800 ( 944) hydrogen bonds : angle 4.08564 ( 2742) Misc. bond : bond 0.00246 ( 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 115 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.862 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 390 MET cc_start: 0.8202 (pmm) cc_final: 0.7614 (pmm) REVERT: f 21 MET cc_start: 0.1301 (mmm) cc_final: 0.0810 (mtt) REVERT: f 29 MET cc_start: 0.1748 (mtp) cc_final: 0.0734 (ttm) REVERT: f 147 MET cc_start: 0.8312 (mmp) cc_final: 0.7559 (mpp) REVERT: f 219 MET cc_start: 0.9147 (mmp) cc_final: 0.8800 (mmt) REVERT: f 380 MET cc_start: 0.9149 (tmm) cc_final: 0.8944 (tmm) REVERT: f 396 MET cc_start: 0.9291 (mmp) cc_final: 0.8786 (mtp) REVERT: c 21 MET cc_start: 0.6202 (mmm) cc_final: 0.5711 (ptm) REVERT: c 29 MET cc_start: -0.0058 (mtp) cc_final: -0.0581 (ttt) REVERT: c 341 MET cc_start: -0.2087 (ttm) cc_final: -0.2776 (tmm) REVERT: c 405 MET cc_start: 0.9024 (ptp) cc_final: 0.8549 (ppp) REVERT: b 21 MET cc_start: 0.3642 (ttt) cc_final: 0.2794 (ttt) REVERT: b 205 MET cc_start: 0.9137 (mpp) cc_final: 0.8773 (tpt) REVERT: b 248 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9067 (mm-30) REVERT: b 390 MET cc_start: 0.4779 (ptm) cc_final: 0.4535 (ptt) REVERT: a 1 MET cc_start: 0.7332 (pmm) cc_final: 0.6995 (pmm) REVERT: a 147 MET cc_start: 0.7093 (tpt) cc_final: 0.6670 (mpp) REVERT: a 219 MET cc_start: 0.9245 (mmp) cc_final: 0.8725 (mmm) REVERT: a 390 MET cc_start: 0.6965 (pmm) cc_final: 0.6397 (pmm) REVERT: d 390 MET cc_start: 0.6198 (ptp) cc_final: 0.5498 (ptt) REVERT: d 396 MET cc_start: 0.9372 (mtp) cc_final: 0.8845 (mtp) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1328 time to fit residues: 25.4644 Evaluate side-chains 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 126 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN f 42 HIS f 126 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 126 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.033756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.026888 restraints weight = 378566.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.027146 restraints weight = 335056.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.027380 restraints weight = 306233.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.027560 restraints weight = 284139.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.027690 restraints weight = 268808.646| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 20379 Z= 0.306 Angle : 0.979 12.990 27469 Z= 0.488 Chirality : 0.050 0.222 3130 Planarity : 0.006 0.050 3524 Dihedral : 10.926 163.377 2901 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.73 % 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 aren not related in a simple way. whole: -0.57 (0.16), residues: 2490 helix: -0.53 (0.14), residues: 1134 sheet: -0.53 (0.26), residues: 402 loop : 0.21 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG f 221 TYR 0.021 0.003 TYR f 332 PHE 0.022 0.003 PHE c 335 TRP 0.012 0.003 TRP e 381 HIS 0.010 0.003 HIS f 344 Details of bonding type rmsd covalent geometry : bond 0.00649 (20349) covalent geometry : angle 0.97899 (27469) hydrogen bonds : bond 0.05251 ( 944) hydrogen bonds : angle 5.05283 ( 2742) Misc. bond : bond 0.00247 ( 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 116 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.851 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: e 380 MET cc_start: 0.9559 (mmp) cc_final: 0.9284 (mmm) REVERT: e 390 MET cc_start: 0.8508 (pmm) cc_final: 0.8228 (pmm) REVERT: e 396 MET cc_start: 0.9435 (ppp) cc_final: 0.9109 (ppp) REVERT: f 21 MET cc_start: 0.1938 (mmm) cc_final: 0.1256 (mtt) REVERT: f 219 MET cc_start: 0.9457 (mmp) cc_final: 0.9256 (mmm) REVERT: c 8 ASN cc_start: 0.9631 (m-40) cc_final: 0.9428 (p0) REVERT: c 29 MET cc_start: 0.1403 (mtp) cc_final: 0.1187 (ttp) REVERT: c 147 MET cc_start: 0.7179 (tpt) cc_final: 0.6488 (mpp) REVERT: c 248 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9415 (mm-30) REVERT: c 341 MET cc_start: -0.0491 (ttm) cc_final: -0.1679 (tmm) REVERT: c 390 MET cc_start: 0.5734 (ptp) cc_final: 0.5341 (pmm) REVERT: b 1 MET cc_start: 0.9155 (pmm) cc_final: 0.8871 (pmm) REVERT: b 21 MET cc_start: 0.4183 (ttt) cc_final: 0.3402 (ttt) REVERT: b 29 MET cc_start: 0.2941 (ttt) cc_final: 0.2255 (tmm) REVERT: b 205 MET cc_start: 0.9211 (mpp) cc_final: 0.8695 (tpt) REVERT: b 341 MET cc_start: 0.1477 (mtp) cc_final: 0.0907 (mpp) REVERT: a 147 MET cc_start: 0.7175 (tpt) cc_final: 0.6492 (mpp) REVERT: a 219 MET cc_start: 0.9521 (mmp) cc_final: 0.8984 (mmm) REVERT: a 390 MET cc_start: 0.7661 (pmm) cc_final: 0.7192 (pmm) REVERT: d 147 MET cc_start: 0.9401 (tpp) cc_final: 0.9021 (tpt) REVERT: d 390 MET cc_start: 0.7207 (ptp) cc_final: 0.6221 (ptt) REVERT: d 396 MET cc_start: 0.9337 (mtp) cc_final: 0.8929 (mtp) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1453 time to fit residues: 27.4812 Evaluate side-chains 101 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 10.0000 chunk 208 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 chunk 155 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 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** b 256 HIS a 25 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 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 = 0.3543 r_free = 0.3543 target = 0.033303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.026705 restraints weight = 378397.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.026904 restraints weight = 337602.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.027193 restraints weight = 312366.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.027377 restraints weight = 278907.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.027615 restraints weight = 257730.280| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20379 Z= 0.160 Angle : 0.657 7.492 27469 Z= 0.325 Chirality : 0.043 0.215 3130 Planarity : 0.004 0.059 3524 Dihedral : 10.272 161.706 2901 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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 aren not related in a simple way. whole: 0.13 (0.17), residues: 2490 helix: 0.27 (0.14), residues: 1152 sheet: -0.41 (0.26), residues: 402 loop : 0.38 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 252 TYR 0.022 0.002 TYR b 332 PHE 0.031 0.002 PHE b 413 TRP 0.004 0.001 TRP c 381 HIS 0.009 0.001 HIS b 239 Details of bonding type rmsd covalent geometry : bond 0.00337 (20349) covalent geometry : angle 0.65726 (27469) hydrogen bonds : bond 0.03265 ( 944) hydrogen bonds : angle 4.42083 ( 2742) Misc. bond : bond 0.00214 ( 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 111 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.828 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 390 MET cc_start: 0.8568 (pmm) cc_final: 0.8019 (pmm) REVERT: e 396 MET cc_start: 0.9326 (ppp) cc_final: 0.8955 (ppp) REVERT: f 21 MET cc_start: 0.2634 (mmm) cc_final: 0.1965 (mtt) REVERT: f 29 MET cc_start: 0.1528 (mtp) cc_final: 0.0955 (ttp) REVERT: f 219 MET cc_start: 0.9457 (mmp) cc_final: 0.9254 (mmm) REVERT: c 147 MET cc_start: 0.7283 (tpt) cc_final: 0.6502 (mpp) REVERT: c 341 MET cc_start: -0.0757 (ttm) cc_final: -0.1707 (tmm) REVERT: c 390 MET cc_start: 0.5601 (ptp) cc_final: 0.5104 (pmm) REVERT: b 21 MET cc_start: 0.4324 (ttt) cc_final: 0.3437 (ttp) REVERT: b 205 MET cc_start: 0.9190 (mpp) cc_final: 0.8497 (tpt) REVERT: b 341 MET cc_start: 0.1269 (mtp) cc_final: 0.0847 (mpp) REVERT: b 390 MET cc_start: 0.6866 (ppp) cc_final: 0.6219 (ppp) REVERT: a 1 MET cc_start: 0.7439 (pmm) cc_final: 0.7175 (pmm) REVERT: a 219 MET cc_start: 0.9481 (mmp) cc_final: 0.8925 (mmm) REVERT: a 390 MET cc_start: 0.7241 (pmm) cc_final: 0.6875 (pmm) REVERT: d 21 MET cc_start: 0.6264 (mpp) cc_final: 0.5025 (ptp) REVERT: d 29 MET cc_start: 0.1570 (ttt) cc_final: 0.1278 (ttt) REVERT: d 147 MET cc_start: 0.9365 (tpp) cc_final: 0.8927 (tpt) REVERT: d 390 MET cc_start: 0.7011 (ptp) cc_final: 0.6188 (ptt) REVERT: d 396 MET cc_start: 0.9326 (mtp) cc_final: 0.8751 (mtp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1332 time to fit residues: 24.4145 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 : 0.830 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 177 optimal weight: 5.9990 chunk 196 optimal weight: 30.0000 chunk 244 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 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 220 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** 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 = 0.3522 r_free = 0.3522 target = 0.032755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.026206 restraints weight = 381438.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.026399 restraints weight = 338672.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.026661 restraints weight = 311301.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.026815 restraints weight = 290637.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.026905 restraints weight = 276098.359| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20379 Z= 0.148 Angle : 0.647 8.226 27469 Z= 0.315 Chirality : 0.043 0.223 3130 Planarity : 0.004 0.052 3524 Dihedral : 10.151 163.840 2901 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.05 % Allowed : 1.26 % Favored : 98.69 % 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 aren not related in a simple way. whole: 0.31 (0.17), residues: 2490 helix: 0.51 (0.15), residues: 1164 sheet: -0.46 (0.27), residues: 360 loop : 0.35 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 252 TYR 0.018 0.001 TYR f 332 PHE 0.022 0.001 PHE b 413 TRP 0.003 0.001 TRP c 381 HIS 0.008 0.001 HIS b 239 Details of bonding type rmsd covalent geometry : bond 0.00311 (20349) covalent geometry : angle 0.64717 (27469) hydrogen bonds : bond 0.03111 ( 944) hydrogen bonds : angle 4.40068 ( 2742) Misc. bond : bond 0.00435 ( 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 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.709 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: e 1 MET cc_start: 0.7146 (ptp) cc_final: 0.6920 (pmm) REVERT: e 390 MET cc_start: 0.8611 (pmm) cc_final: 0.8061 (pmm) REVERT: e 396 MET cc_start: 0.9322 (ppp) cc_final: 0.8912 (ppp) REVERT: f 21 MET cc_start: 0.3030 (mmm) cc_final: 0.2407 (mtt) REVERT: f 29 MET cc_start: 0.1781 (mtp) cc_final: 0.1001 (ttp) REVERT: f 219 MET cc_start: 0.9360 (mmp) cc_final: 0.9150 (mmm) REVERT: c 1 MET cc_start: 0.7593 (ptp) cc_final: 0.7194 (ptp) REVERT: c 8 ASN cc_start: 0.9626 (m-40) cc_final: 0.9391 (p0) REVERT: c 341 MET cc_start: -0.0402 (ttm) cc_final: -0.1390 (tmm) REVERT: b 21 MET cc_start: 0.4523 (ttt) cc_final: 0.3841 (ttm) REVERT: b 29 MET cc_start: 0.2746 (ptm) cc_final: 0.2390 (tmm) REVERT: b 205 MET cc_start: 0.9126 (mpp) cc_final: 0.8413 (tpt) REVERT: b 341 MET cc_start: 0.1720 (mtp) cc_final: 0.1107 (mpp) REVERT: b 390 MET cc_start: 0.6729 (ppp) cc_final: 0.5963 (ppp) REVERT: a 1 MET cc_start: 0.7519 (pmm) cc_final: 0.7217 (pmm) REVERT: a 219 MET cc_start: 0.9404 (mmp) cc_final: 0.8837 (mmm) REVERT: a 390 MET cc_start: 0.7314 (pmm) cc_final: 0.6923 (pmm) REVERT: d 29 MET cc_start: 0.1386 (ttt) cc_final: 0.1096 (ttt) REVERT: d 147 MET cc_start: 0.9381 (tpp) cc_final: 0.8960 (tpt) REVERT: d 390 MET cc_start: 0.7022 (ptp) cc_final: 0.6156 (ptt) REVERT: d 396 MET cc_start: 0.9329 (mtp) cc_final: 0.8720 (mtp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1292 time to fit residues: 22.9147 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 : 0.902 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 113 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 ASN ** f 189 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 ** 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 = 0.3536 r_free = 0.3536 target = 0.033073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.026523 restraints weight = 377746.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.026714 restraints weight = 333050.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.026987 restraints weight = 306776.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.027156 restraints weight = 286592.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.027241 restraints weight = 270397.417| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20379 Z= 0.103 Angle : 0.594 9.283 27469 Z= 0.284 Chirality : 0.042 0.179 3130 Planarity : 0.004 0.044 3524 Dihedral : 9.924 163.961 2901 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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 aren not related in a simple way. whole: 0.73 (0.17), residues: 2490 helix: 0.92 (0.15), residues: 1158 sheet: -0.10 (0.27), residues: 372 loop : 0.40 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 30 TYR 0.017 0.001 TYR f 332 PHE 0.019 0.001 PHE f 121 TRP 0.005 0.001 TRP c 381 HIS 0.007 0.001 HIS b 239 Details of bonding type rmsd covalent geometry : bond 0.00215 (20349) covalent geometry : angle 0.59373 (27469) hydrogen bonds : bond 0.02704 ( 944) hydrogen bonds : angle 4.16699 ( 2742) Misc. bond : bond 0.00324 ( 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 : 0.693 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 390 MET cc_start: 0.8574 (pmm) cc_final: 0.8025 (pmm) REVERT: e 396 MET cc_start: 0.9318 (ppp) cc_final: 0.8894 (ppp) REVERT: f 1 MET cc_start: 0.6877 (pmm) cc_final: 0.5394 (ptt) REVERT: f 21 MET cc_start: 0.2830 (mmm) cc_final: 0.2177 (mtt) REVERT: f 29 MET cc_start: 0.1342 (mtp) cc_final: 0.0513 (ttp) REVERT: f 396 MET cc_start: 0.9330 (mmp) cc_final: 0.8787 (mtp) REVERT: c 390 MET cc_start: 0.5308 (ptp) cc_final: 0.5011 (pmm) REVERT: b 21 MET cc_start: 0.4342 (ttt) cc_final: 0.3751 (ttm) REVERT: b 29 MET cc_start: 0.2370 (ptm) cc_final: 0.2131 (tmm) REVERT: b 205 MET cc_start: 0.9119 (mpp) cc_final: 0.8483 (tpt) REVERT: b 245 MET cc_start: 0.9047 (ptp) cc_final: 0.8833 (ptt) REVERT: b 341 MET cc_start: 0.1461 (mtp) cc_final: 0.1018 (mpp) REVERT: b 390 MET cc_start: 0.6509 (ppp) cc_final: 0.5510 (ppp) REVERT: a 1 MET cc_start: 0.6994 (pmm) cc_final: 0.6660 (pmm) REVERT: a 29 MET cc_start: -0.2897 (ttp) cc_final: -0.3500 (ttt) REVERT: a 219 MET cc_start: 0.9290 (mmp) cc_final: 0.8782 (mmm) REVERT: a 390 MET cc_start: 0.7081 (pmm) cc_final: 0.6719 (pmm) REVERT: d 29 MET cc_start: 0.1363 (ttt) cc_final: 0.1058 (ttt) REVERT: d 147 MET cc_start: 0.9373 (tpp) cc_final: 0.8976 (tpt) REVERT: d 390 MET cc_start: 0.6954 (ptp) cc_final: 0.6170 (ptt) REVERT: d 396 MET cc_start: 0.9334 (mtp) cc_final: 0.8712 (mtp) REVERT: d 416 MET cc_start: 0.5441 (ptt) cc_final: 0.5185 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1403 time to fit residues: 24.6796 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 : 0.746 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 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 = 0.3513 r_free = 0.3513 target = 0.032377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.025857 restraints weight = 385037.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.026121 restraints weight = 339284.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.026359 restraints weight = 310443.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.026493 restraints weight = 291473.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.026543 restraints weight = 278120.498| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20379 Z= 0.121 Angle : 0.612 8.561 27469 Z= 0.297 Chirality : 0.042 0.156 3130 Planarity : 0.004 0.041 3524 Dihedral : 9.891 164.306 2901 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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 aren not related in a simple way. whole: 0.84 (0.17), residues: 2490 helix: 1.06 (0.15), residues: 1152 sheet: -0.05 (0.28), residues: 372 loop : 0.42 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 30 TYR 0.014 0.001 TYR f 332 PHE 0.014 0.001 PHE f 121 TRP 0.002 0.000 TRP e 381 HIS 0.007 0.001 HIS b 239 Details of bonding type rmsd covalent geometry : bond 0.00256 (20349) covalent geometry : angle 0.61201 (27469) hydrogen bonds : bond 0.02847 ( 944) hydrogen bonds : angle 4.23212 ( 2742) Misc. bond : bond 0.00297 ( 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 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.875 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 390 MET cc_start: 0.8570 (pmm) cc_final: 0.7980 (pmm) REVERT: e 396 MET cc_start: 0.9332 (ppp) cc_final: 0.8949 (ppp) REVERT: f 29 MET cc_start: 0.1882 (mtp) cc_final: 0.1232 (ttp) REVERT: f 219 MET cc_start: 0.9298 (mmp) cc_final: 0.9083 (mmm) REVERT: f 396 MET cc_start: 0.9346 (mmp) cc_final: 0.8805 (mtp) REVERT: c 341 MET cc_start: -0.0324 (ttm) cc_final: -0.1342 (tmm) REVERT: b 21 MET cc_start: 0.4150 (ttt) cc_final: 0.3471 (ttm) REVERT: b 205 MET cc_start: 0.9208 (mpp) cc_final: 0.8419 (tpt) REVERT: b 341 MET cc_start: 0.1750 (mtp) cc_final: 0.1459 (mtm) REVERT: b 390 MET cc_start: 0.6934 (ppp) cc_final: 0.6306 (ppp) REVERT: a 1 MET cc_start: 0.7189 (pmm) cc_final: 0.6831 (pmm) REVERT: a 219 MET cc_start: 0.9404 (mmp) cc_final: 0.8916 (mmm) REVERT: a 327 MET cc_start: 0.8755 (mmp) cc_final: 0.8466 (mmm) REVERT: a 390 MET cc_start: 0.7197 (pmm) cc_final: 0.6836 (pmm) REVERT: a 396 MET cc_start: 0.9043 (ppp) cc_final: 0.8824 (ppp) REVERT: d 29 MET cc_start: 0.1695 (ttt) cc_final: 0.1365 (ttt) REVERT: d 147 MET cc_start: 0.9386 (tpp) cc_final: 0.8992 (tpt) REVERT: d 245 MET cc_start: 0.8447 (ptt) cc_final: 0.7989 (ptt) REVERT: d 390 MET cc_start: 0.6878 (ptp) cc_final: 0.6023 (ptt) REVERT: d 396 MET cc_start: 0.9351 (mtp) cc_final: 0.9133 (mtt) REVERT: d 416 MET cc_start: 0.5824 (ptt) cc_final: 0.5561 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1527 time to fit residues: 26.0001 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 : 0.912 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.030897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.024704 restraints weight = 390347.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.024916 restraints weight = 342136.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.025171 restraints weight = 313091.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.025283 restraints weight = 289204.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.025457 restraints weight = 275030.634| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.8881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20379 Z= 0.145 Angle : 0.655 10.062 27469 Z= 0.320 Chirality : 0.043 0.217 3130 Planarity : 0.004 0.044 3524 Dihedral : 10.026 166.147 2901 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 aren not related in a simple way. whole: 0.76 (0.17), residues: 2490 helix: 1.03 (0.15), residues: 1152 sheet: -0.15 (0.27), residues: 378 loop : 0.33 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 366 TYR 0.017 0.002 TYR f 332 PHE 0.026 0.002 PHE b 413 TRP 0.004 0.001 TRP f 381 HIS 0.021 0.001 HIS e 344 Details of bonding type rmsd covalent geometry : bond 0.00306 (20349) covalent geometry : angle 0.65504 (27469) hydrogen bonds : bond 0.03068 ( 944) hydrogen bonds : angle 4.35934 ( 2742) Misc. bond : bond 0.00290 ( 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 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.816 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: e 29 MET cc_start: 0.3919 (ptm) cc_final: 0.3551 (tmm) REVERT: e 390 MET cc_start: 0.8682 (pmm) cc_final: 0.8373 (pmm) REVERT: e 396 MET cc_start: 0.9368 (ppp) cc_final: 0.8950 (ppp) REVERT: f 29 MET cc_start: 0.2394 (mtp) cc_final: 0.1873 (ttp) REVERT: f 219 MET cc_start: 0.9358 (mmp) cc_final: 0.9106 (mmm) REVERT: f 396 MET cc_start: 0.9312 (mmp) cc_final: 0.8720 (mtp) REVERT: c 327 MET cc_start: 0.9018 (mmm) cc_final: 0.8240 (tpt) REVERT: c 341 MET cc_start: 0.0054 (ttm) cc_final: -0.0957 (tmm) REVERT: c 390 MET cc_start: 0.7070 (pmm) cc_final: 0.6773 (pmm) REVERT: b 21 MET cc_start: 0.4369 (ttt) cc_final: 0.3499 (ttt) REVERT: b 205 MET cc_start: 0.9187 (mpp) cc_final: 0.8358 (tpt) REVERT: b 341 MET cc_start: 0.2194 (mtp) cc_final: 0.1918 (mtm) REVERT: b 390 MET cc_start: 0.7592 (ppp) cc_final: 0.7028 (ppp) REVERT: a 147 MET cc_start: 0.6833 (tpt) cc_final: 0.6115 (mpp) REVERT: a 219 MET cc_start: 0.9301 (mmp) cc_final: 0.8801 (mmm) REVERT: a 327 MET cc_start: 0.8859 (mmp) cc_final: 0.8627 (mmm) REVERT: a 390 MET cc_start: 0.7462 (pmm) cc_final: 0.7136 (pmm) REVERT: d 1 MET cc_start: 0.7574 (ptt) cc_final: 0.7112 (ptp) REVERT: d 29 MET cc_start: 0.1099 (ttt) cc_final: 0.0780 (ttt) REVERT: d 147 MET cc_start: 0.9327 (tpp) cc_final: 0.8872 (tpt) REVERT: d 390 MET cc_start: 0.7141 (ptp) cc_final: 0.6285 (ptt) REVERT: d 396 MET cc_start: 0.9344 (mtp) cc_final: 0.8851 (mtp) REVERT: d 416 MET cc_start: 0.6230 (ptt) cc_final: 0.5877 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1413 time to fit residues: 24.2518 Evaluate side-chains 97 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 240 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 20 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 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 = 0.3427 r_free = 0.3427 target = 0.029697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.023679 restraints weight = 398630.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.023882 restraints weight = 347065.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.024184 restraints weight = 313252.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.024454 restraints weight = 267464.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.024456 restraints weight = 237248.380| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.9701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20379 Z= 0.159 Angle : 0.675 11.265 27469 Z= 0.330 Chirality : 0.043 0.159 3130 Planarity : 0.005 0.169 3524 Dihedral : 10.038 165.359 2901 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 aren not related in a simple way. whole: 0.60 (0.17), residues: 2490 helix: 0.89 (0.15), residues: 1164 sheet: -0.33 (0.27), residues: 360 loop : 0.30 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 366 TYR 0.021 0.002 TYR e 332 PHE 0.031 0.002 PHE c 335 TRP 0.004 0.001 TRP f 381 HIS 0.007 0.001 HIS f 140 Details of bonding type rmsd covalent geometry : bond 0.00332 (20349) covalent geometry : angle 0.67521 (27469) hydrogen bonds : bond 0.03206 ( 944) hydrogen bonds : angle 4.48093 ( 2742) Misc. bond : bond 0.00274 ( 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 103 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.903 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: e 390 MET cc_start: 0.8701 (pmm) cc_final: 0.8420 (pmm) REVERT: e 396 MET cc_start: 0.9373 (ppp) cc_final: 0.8963 (ppp) REVERT: f 29 MET cc_start: 0.2439 (mtp) cc_final: 0.1793 (ttp) REVERT: f 219 MET cc_start: 0.9444 (mmp) cc_final: 0.9189 (mmm) REVERT: f 396 MET cc_start: 0.9348 (mmp) cc_final: 0.8830 (mtp) REVERT: c 341 MET cc_start: 0.0719 (ttm) cc_final: 0.0074 (tmm) REVERT: c 390 MET cc_start: 0.7352 (pmm) cc_final: 0.6967 (pmm) REVERT: b 29 MET cc_start: 0.4966 (tmm) cc_final: 0.4486 (ppp) REVERT: b 205 MET cc_start: 0.9182 (mpp) cc_final: 0.8267 (tpt) REVERT: b 341 MET cc_start: 0.3030 (mtp) cc_final: 0.2734 (mtm) REVERT: b 390 MET cc_start: 0.7876 (ppp) cc_final: 0.7356 (ppp) REVERT: a 1 MET cc_start: 0.6891 (pmm) cc_final: 0.6519 (ptp) REVERT: a 29 MET cc_start: -0.1576 (ptm) cc_final: -0.2201 (ptm) REVERT: a 219 MET cc_start: 0.9387 (mmp) cc_final: 0.8947 (mmm) REVERT: d 29 MET cc_start: 0.1436 (ttt) cc_final: 0.1090 (ttt) REVERT: d 147 MET cc_start: 0.9303 (tpp) cc_final: 0.8883 (tpt) REVERT: d 245 MET cc_start: 0.8534 (ptt) cc_final: 0.8118 (ptt) REVERT: d 327 MET cc_start: 0.8735 (tpt) cc_final: 0.8527 (tpp) REVERT: d 390 MET cc_start: 0.7278 (ptp) cc_final: 0.6417 (ptt) REVERT: d 396 MET cc_start: 0.9363 (mtp) cc_final: 0.8854 (mtp) REVERT: d 416 MET cc_start: 0.6974 (ptt) cc_final: 0.6742 (ptt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1321 time to fit residues: 22.3254 Evaluate side-chains 98 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 0.0060 chunk 171 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN ** a 239 HIS ** 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 = 0.3421 r_free = 0.3421 target = 0.029415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.023403 restraints weight = 397692.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.023598 restraints weight = 347761.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.023771 restraints weight = 314643.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.023998 restraints weight = 291904.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.024212 restraints weight = 269020.355| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 1.0022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20379 Z= 0.120 Angle : 0.610 8.908 27469 Z= 0.297 Chirality : 0.043 0.215 3130 Planarity : 0.004 0.046 3524 Dihedral : 9.836 164.761 2901 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 aren not related in a simple way. whole: 0.76 (0.17), residues: 2490 helix: 1.09 (0.15), residues: 1164 sheet: -0.07 (0.27), residues: 372 loop : 0.21 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 366 TYR 0.012 0.001 TYR b 332 PHE 0.020 0.001 PHE b 413 TRP 0.004 0.001 TRP b 381 HIS 0.007 0.001 HIS b 239 Details of bonding type rmsd covalent geometry : bond 0.00255 (20349) covalent geometry : angle 0.60994 (27469) hydrogen bonds : bond 0.02807 ( 944) hydrogen bonds : angle 4.33617 ( 2742) Misc. bond : bond 0.00262 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.34 seconds wall clock time: 68 minutes 38.76 seconds (4118.76 seconds total)