Starting phenix.real_space_refine on Sun Aug 24 13:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5l_27914/08_2025/8e5l_27914_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 21 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12533 2.51 5 N 3540 2.21 5 O 3832 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s 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: 20058 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.82, per 1000 atoms: 0.24 Number of scatterers: 20058 At special positions: 0 Unit cell: (145.32, 126.636, 137.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 21 15.00 Mg 6 11.99 F 18 9.00 O 3832 8.00 N 3540 7.00 C 12533 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 Creating SS restraints... Processing helix chain 'e' and resid 2 through 9 Processing helix chain 'e' and resid 10 through 22 Processing helix chain 'e' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 132 through 136 Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 235 through 255 Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 338 removed outlier: 3.554A pdb=" N GLU e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 371 Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 391 through 404 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS e 417 " --> pdb=" O PHE e 413 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 Processing helix chain 'f' and resid 10 through 22 Processing helix chain 'f' and resid 30 through 45 removed outlier: 3.705A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 90 Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 132 through 136 Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 221 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 335 removed outlier: 3.717A pdb=" N GLU f 329 " --> pdb=" O SER f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 371 Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 391 through 404 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.718A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS f 417 " --> pdb=" O PHE f 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 Processing helix chain 'c' and resid 10 through 22 Processing helix chain 'c' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 90 Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.270A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 221 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU c 333 " --> pdb=" O GLU c 329 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 371 Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 391 through 404 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS c 417 " --> pdb=" O PHE c 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 Processing helix chain 'b' and resid 10 through 22 Processing helix chain 'b' and resid 30 through 45 removed outlier: 3.704A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 90 Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 132 through 136 Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 221 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 335 removed outlier: 3.643A pdb=" N GLU b 333 " --> pdb=" O GLU b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 391 through 404 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.722A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS b 417 " --> pdb=" O PHE b 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 10 through 22 Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.702A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 90 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 132 through 136 Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 221 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 337 removed outlier: 4.203A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 371 Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 391 through 404 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS a 417 " --> pdb=" O PHE a 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 Processing helix chain 'd' and resid 10 through 22 Processing helix chain 'd' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 90 Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.267A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 221 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 333 Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 371 Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 391 through 404 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR e 96 " --> pdb=" O VAL e 119 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL e 119 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER e 98 " --> pdb=" O ASN e 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS e 115 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG e 102 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.802A pdb=" N ASN e 306 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.476A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA e 317 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU e 342 " --> pdb=" O GLY e 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY e 364 " --> pdb=" O GLU e 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR f 96 " --> pdb=" O VAL f 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL f 119 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER f 98 " --> pdb=" O ASN f 117 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS f 115 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG f 102 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU f 113 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.805A pdb=" N ASN f 306 " --> pdb=" O LEU f 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.480A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA f 317 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU f 342 " --> pdb=" O GLY f 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY f 364 " --> pdb=" O GLU f 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR c 96 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL c 119 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER c 98 " --> pdb=" O ASN c 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS c 115 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG c 102 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN c 306 " --> pdb=" O LEU c 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.479A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA c 317 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU c 342 " --> pdb=" O GLY c 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY c 364 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR b 96 " --> pdb=" O VAL b 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 119 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 98 " --> pdb=" O ASN b 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS b 115 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG b 102 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU b 113 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN b 306 " --> pdb=" O LEU b 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA b 317 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU b 342 " --> pdb=" O GLY b 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY b 364 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'a' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR a 96 " --> pdb=" O VAL a 119 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL a 119 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER a 98 " --> pdb=" O ASN a 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS a 115 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG a 102 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN a 306 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA a 317 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU a 342 " --> pdb=" O GLY a 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY a 364 " --> pdb=" O GLU a 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR d 96 " --> pdb=" O VAL d 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL d 119 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER d 98 " --> pdb=" O ASN d 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS d 115 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG d 102 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU d 113 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.806A pdb=" N ASN d 306 " --> pdb=" O LEU d 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA d 317 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 364 " --> pdb=" O GLU d 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 944 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 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: 4755 1.33 - 1.45: 3619 1.45 - 1.57: 11764 1.57 - 1.69: 35 1.69 - 1.81: 198 Bond restraints: 20371 Sorted by residual: bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF f1002 " pdb="BE BEF f1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 27286 2.88 - 5.77: 167 5.77 - 8.65: 38 8.65 - 11.53: 6 11.53 - 14.41: 6 Bond angle restraints: 27503 Sorted by residual: angle pdb=" N ASP f 322 " pdb=" CA ASP f 322 " pdb=" C ASP f 322 " ideal model delta sigma weight residual 112.58 105.31 7.27 1.22e+00 6.72e-01 3.55e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.73 6.60 1.21e+00 6.83e-01 2.97e+01 angle pdb=" N GLU c 334 " pdb=" CA GLU c 334 " pdb=" C GLU c 334 " ideal model delta sigma weight residual 111.33 105.04 6.29 1.21e+00 6.83e-01 2.70e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 12396 29.81 - 59.62: 154 59.62 - 89.43: 45 89.43 - 119.24: 2 119.24 - 149.05: 10 Dihedral angle restraints: 12607 sinusoidal: 5413 harmonic: 7194 Sorted by residual: dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.05 -149.05 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP e1000 " pdb=" O3A ADP e1000 " pdb=" PB ADP e1000 " pdb=" PA ADP e1000 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.98 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PA ADP d1000 " pdb=" PB ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 84.41 -144.41 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2600 0.052 - 0.103: 412 0.103 - 0.155: 112 0.155 - 0.206: 10 0.206 - 0.258: 1 Chirality restraints: 3135 Sorted by residual: chirality pdb=" C3' A 7 1 " pdb=" C4' A 7 1 " pdb=" O3' A 7 1 " pdb=" C2' A 7 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL d 330 " pdb=" N VAL d 330 " pdb=" C VAL d 330 " pdb=" CB VAL d 330 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" C3' U 7 2 " pdb=" C4' U 7 2 " pdb=" O3' U 7 2 " pdb=" C2' U 7 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3132 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.48e-02 4.19e+01 pdb=" C ILE b 331 " -0.112 2.00e-02 2.50e+03 pdb=" O ILE b 331 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR b 332 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 331 " -0.028 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C ILE e 331 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE e 331 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR e 332 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 331 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE c 331 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE c 331 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR c 332 " 0.028 2.00e-02 2.50e+03 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 55 2.02 - 2.74: 1642 2.74 - 3.46: 29057 3.46 - 4.18: 46275 4.18 - 4.90: 83659 Nonbonded interactions: 160688 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 3.040 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 nonbonded pdb=" NH1 ARG e 272 " pdb=" OE2 GLU f 334 " model vdw 1.416 3.120 nonbonded pdb=" NZ LYS e 385 " pdb=" O LYS d 352 " model vdw 1.495 3.120 ... (remaining 160683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.590 Find NCS groups from input model: 0.400 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.748 20401 Z= 1.843 Angle : 0.641 14.413 27503 Z= 0.351 Chirality : 0.042 0.258 3135 Planarity : 0.004 0.065 3525 Dihedral : 11.889 149.051 7951 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 4.11 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 0.016 0.001 TYR d 332 PHE 0.007 0.001 PHE a 36 TRP 0.003 0.001 TRP a 381 HIS 0.001 0.000 HIS e 295 Details of bonding type rmsd covalent geometry : bond 0.00342 (20371) covalent geometry : angle 0.64137 (27503) hydrogen bonds : bond 0.19912 ( 944) hydrogen bonds : angle 6.53638 ( 2742) Misc. bond : bond 0.47746 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.1134 (mmm) cc_final: -0.0696 (ttt) REVERT: c 29 MET cc_start: -0.1502 (mtp) cc_final: -0.2170 (ttt) REVERT: b 29 MET cc_start: -0.1529 (mtp) cc_final: -0.2116 (ttt) REVERT: d 21 MET cc_start: -0.0973 (mmm) cc_final: -0.4034 (ttt) outliers start: 35 outliers final: 8 residues processed: 269 average time/residue: 0.1712 time to fit residues: 68.2371 Evaluate side-chains 147 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 135 ASN e 220 GLN e 241 GLN e 256 HIS f 126 ASN f 256 HIS c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 ASN ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN c 295 HIS c 340 ASN b 25 ASN b 220 GLN b 241 GLN b 256 HIS a 142 ASN a 256 HIS d 135 ASN d 241 GLN d 256 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.034060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.027109 restraints weight = 335869.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.027696 restraints weight = 259386.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.028119 restraints weight = 213804.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.028433 restraints weight = 184873.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.028619 restraints weight = 165300.620| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20401 Z= 0.246 Angle : 0.829 10.111 27503 Z= 0.409 Chirality : 0.046 0.193 3135 Planarity : 0.006 0.051 3525 Dihedral : 11.062 162.131 2917 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.33 % Allowed : 3.13 % Favored : 96.55 % 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: -0.33 (0.16), residues: 2490 helix: 0.04 (0.14), residues: 1164 sheet: -0.87 (0.25), residues: 402 loop : 0.04 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG c 66 TYR 0.025 0.003 TYR d 332 PHE 0.019 0.002 PHE b 335 TRP 0.019 0.002 TRP d 381 HIS 0.013 0.003 HIS c 388 Details of bonding type rmsd covalent geometry : bond 0.00505 (20371) covalent geometry : angle 0.82910 (27503) hydrogen bonds : bond 0.04230 ( 944) hydrogen bonds : angle 4.91071 ( 2742) Misc. bond : bond 0.00302 ( 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 153 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.853 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: e 21 MET cc_start: -0.0897 (ttt) cc_final: -0.1154 (ttt) REVERT: e 207 LEU cc_start: 0.9364 (mp) cc_final: 0.9002 (mp) REVERT: e 413 PHE cc_start: 0.3484 (OUTLIER) cc_final: 0.2752 (m-80) REVERT: f 21 MET cc_start: -0.1865 (mmm) cc_final: -0.2539 (mtm) REVERT: f 29 MET cc_start: 0.2619 (ttm) cc_final: 0.2380 (ttm) REVERT: f 36 PHE cc_start: 0.9241 (t80) cc_final: 0.9037 (t80) REVERT: f 147 MET cc_start: 0.8618 (mmp) cc_final: 0.8122 (mpp) REVERT: f 219 MET cc_start: 0.9412 (mmp) cc_final: 0.8966 (mmm) REVERT: f 396 MET cc_start: 0.9209 (mmp) cc_final: 0.8969 (mmm) REVERT: f 413 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: c 1 MET cc_start: 0.9282 (mpp) cc_final: 0.8376 (mpp) REVERT: c 416 MET cc_start: 0.4696 (ptm) cc_final: 0.4195 (ptt) REVERT: b 29 MET cc_start: 0.2700 (mtp) cc_final: 0.2003 (ttt) REVERT: b 111 PHE cc_start: 0.9036 (m-80) cc_final: 0.8588 (m-80) REVERT: a 132 LEU cc_start: 0.9708 (mt) cc_final: 0.9507 (mt) REVERT: a 147 MET cc_start: 0.8741 (tpp) cc_final: 0.8161 (tpp) REVERT: a 327 MET cc_start: 0.9253 (ttp) cc_final: 0.8985 (tmm) REVERT: d 21 MET cc_start: -0.4145 (mmm) cc_final: -0.4466 (mtt) REVERT: d 29 MET cc_start: 0.8761 (ttp) cc_final: 0.8462 (ptm) REVERT: d 147 MET cc_start: 0.8410 (mmp) cc_final: 0.7481 (tpt) REVERT: d 380 MET cc_start: 0.9031 (mmp) cc_final: 0.8830 (mmm) outliers start: 7 outliers final: 2 residues processed: 153 average time/residue: 0.1471 time to fit residues: 35.9094 Evaluate side-chains 122 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 147 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 GLN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS c 388 HIS ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 GLN a 239 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.034200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.027348 restraints weight = 332417.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.027985 restraints weight = 249200.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.028427 restraints weight = 201210.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.028754 restraints weight = 171540.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.028994 restraints weight = 151902.279| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20401 Z= 0.131 Angle : 0.603 6.841 27503 Z= 0.291 Chirality : 0.042 0.146 3135 Planarity : 0.004 0.043 3525 Dihedral : 10.268 167.721 2917 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 0.46 (0.17), residues: 2490 helix: 0.74 (0.15), residues: 1182 sheet: -0.57 (0.26), residues: 396 loop : 0.41 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 66 TYR 0.017 0.001 TYR f 332 PHE 0.025 0.001 PHE f 36 TRP 0.010 0.001 TRP d 381 HIS 0.008 0.001 HIS c 388 Details of bonding type rmsd covalent geometry : bond 0.00266 (20371) covalent geometry : angle 0.60311 (27503) hydrogen bonds : bond 0.02775 ( 944) hydrogen bonds : angle 4.26409 ( 2742) Misc. bond : bond 0.00272 ( 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 131 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 MET cc_start: 0.4915 (ttm) cc_final: 0.4474 (ttt) REVERT: e 207 LEU cc_start: 0.9194 (mp) cc_final: 0.8982 (mp) REVERT: e 327 MET cc_start: 0.9541 (tmm) cc_final: 0.9280 (tmm) REVERT: f 1 MET cc_start: 0.4575 (pmm) cc_final: 0.4286 (pmm) REVERT: f 21 MET cc_start: -0.1101 (mmm) cc_final: -0.2262 (mtm) REVERT: f 219 MET cc_start: 0.9138 (mmp) cc_final: 0.8781 (mmm) REVERT: f 396 MET cc_start: 0.9079 (mmp) cc_final: 0.8868 (mmm) REVERT: c 1 MET cc_start: 0.9263 (mpp) cc_final: 0.8936 (mpp) REVERT: c 147 MET cc_start: 0.6283 (tpt) cc_final: 0.5485 (mpp) REVERT: b 29 MET cc_start: 0.2570 (mtp) cc_final: 0.1869 (ttt) REVERT: b 111 PHE cc_start: 0.8867 (m-80) cc_final: 0.8412 (m-80) REVERT: b 147 MET cc_start: 0.5376 (tpt) cc_final: 0.5121 (mpp) REVERT: a 327 MET cc_start: 0.9172 (ttp) cc_final: 0.8870 (tmm) REVERT: d 21 MET cc_start: -0.3859 (mmm) cc_final: -0.4092 (mtt) REVERT: d 29 MET cc_start: 0.8716 (ttp) cc_final: 0.8323 (ptm) REVERT: d 147 MET cc_start: 0.8501 (mmp) cc_final: 0.7695 (tpt) REVERT: d 186 MET cc_start: 0.9305 (tmm) cc_final: 0.9012 (tmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1598 time to fit residues: 33.2558 Evaluate side-chains 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 117 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN e 142 ASN ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 GLN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 388 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 ASN ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 ASN d 190 ASN ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.029132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.022840 restraints weight = 359455.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.023389 restraints weight = 271789.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.023782 restraints weight = 220283.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.024079 restraints weight = 188369.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.024299 restraints weight = 166927.075| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20401 Z= 0.246 Angle : 0.775 11.163 27503 Z= 0.391 Chirality : 0.045 0.196 3135 Planarity : 0.005 0.047 3525 Dihedral : 10.626 172.461 2917 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % 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: -0.25 (0.16), residues: 2490 helix: 0.01 (0.14), residues: 1176 sheet: -0.75 (0.26), residues: 390 loop : 0.18 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 221 TYR 0.021 0.003 TYR f 332 PHE 0.029 0.002 PHE f 36 TRP 0.005 0.001 TRP a 381 HIS 0.010 0.002 HIS f 42 Details of bonding type rmsd covalent geometry : bond 0.00482 (20371) covalent geometry : angle 0.77457 (27503) hydrogen bonds : bond 0.04095 ( 944) hydrogen bonds : angle 4.93316 ( 2742) Misc. bond : bond 0.00275 ( 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 127 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.8413 (ptp) cc_final: 0.7809 (ptp) REVERT: e 21 MET cc_start: -0.0915 (ttt) cc_final: -0.1207 (ttt) REVERT: e 147 MET cc_start: 0.7667 (mpp) cc_final: 0.6907 (mpp) REVERT: e 207 LEU cc_start: 0.9488 (mp) cc_final: 0.9283 (mp) REVERT: f 1 MET cc_start: 0.5560 (pmm) cc_final: 0.5346 (pmm) REVERT: f 29 MET cc_start: 0.2850 (ttm) cc_final: 0.2487 (ptm) REVERT: f 207 LEU cc_start: 0.9318 (pt) cc_final: 0.8975 (tp) REVERT: f 219 MET cc_start: 0.9248 (mmp) cc_final: 0.8985 (mmm) REVERT: f 341 MET cc_start: 0.5345 (tmm) cc_final: 0.4903 (tmm) REVERT: f 396 MET cc_start: 0.9163 (mmp) cc_final: 0.8837 (mmm) REVERT: c 147 MET cc_start: 0.6243 (tpt) cc_final: 0.5685 (mpp) REVERT: c 390 MET cc_start: 0.8848 (ptt) cc_final: 0.8581 (ptt) REVERT: b 8 ASN cc_start: 0.9334 (m-40) cc_final: 0.8959 (p0) REVERT: b 29 MET cc_start: 0.4762 (mtp) cc_final: 0.4434 (ttp) REVERT: a 1 MET cc_start: 0.8020 (pmm) cc_final: 0.7773 (pmm) REVERT: a 29 MET cc_start: 0.3815 (ttp) cc_final: 0.3173 (ptm) REVERT: a 147 MET cc_start: 0.6791 (tpt) cc_final: 0.5775 (mpp) REVERT: a 245 MET cc_start: 0.9394 (ptp) cc_final: 0.8699 (ptp) REVERT: d 8 ASN cc_start: 0.9354 (m-40) cc_final: 0.9083 (p0) REVERT: d 186 MET cc_start: 0.9452 (tmm) cc_final: 0.9154 (tmm) REVERT: d 390 MET cc_start: 0.8774 (pmm) cc_final: 0.8570 (pmm) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1528 time to fit residues: 31.0718 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 : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS e 241 GLN f 32 GLN f 41 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN a 32 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.029868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.023556 restraints weight = 347710.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.024131 restraints weight = 258167.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.024548 restraints weight = 206827.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.024855 restraints weight = 175454.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.025079 restraints weight = 154579.997| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20401 Z= 0.124 Angle : 0.609 6.782 27503 Z= 0.294 Chirality : 0.042 0.138 3135 Planarity : 0.004 0.035 3525 Dihedral : 10.149 170.460 2917 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2490 helix: 0.60 (0.14), residues: 1176 sheet: -0.60 (0.26), residues: 384 loop : 0.32 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 221 TYR 0.020 0.002 TYR c 332 PHE 0.010 0.001 PHE f 36 TRP 0.006 0.001 TRP b 381 HIS 0.008 0.001 HIS e 344 Details of bonding type rmsd covalent geometry : bond 0.00261 (20371) covalent geometry : angle 0.60858 (27503) hydrogen bonds : bond 0.02831 ( 944) hydrogen bonds : angle 4.45391 ( 2742) Misc. bond : bond 0.00266 ( 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 121 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 207 LEU cc_start: 0.9522 (mp) cc_final: 0.9272 (mp) REVERT: f 1 MET cc_start: 0.5635 (pmm) cc_final: 0.5324 (pmm) REVERT: f 219 MET cc_start: 0.9134 (mmp) cc_final: 0.8796 (mmm) REVERT: f 396 MET cc_start: 0.9167 (mmp) cc_final: 0.8917 (mtp) REVERT: c 147 MET cc_start: 0.6289 (tpt) cc_final: 0.5781 (mpp) REVERT: c 390 MET cc_start: 0.8868 (ptt) cc_final: 0.8486 (ptt) REVERT: b 8 ASN cc_start: 0.9299 (m-40) cc_final: 0.8912 (p0) REVERT: b 29 MET cc_start: 0.4748 (mtp) cc_final: 0.4013 (mtp) REVERT: b 111 PHE cc_start: 0.9148 (m-80) cc_final: 0.8583 (m-80) REVERT: b 147 MET cc_start: 0.8411 (mpp) cc_final: 0.7077 (tpt) REVERT: a 1 MET cc_start: 0.7885 (pmm) cc_final: 0.7639 (pmm) REVERT: a 29 MET cc_start: 0.2968 (ttp) cc_final: 0.2481 (ptm) REVERT: a 147 MET cc_start: 0.6821 (tpt) cc_final: 0.6023 (mpp) REVERT: a 390 MET cc_start: 0.9020 (ptm) cc_final: 0.8815 (ptt) REVERT: d 8 ASN cc_start: 0.9387 (m-40) cc_final: 0.9128 (p0) REVERT: d 147 MET cc_start: 0.8417 (mmp) cc_final: 0.7675 (tpt) REVERT: d 186 MET cc_start: 0.9466 (tmm) cc_final: 0.9178 (tmm) REVERT: d 390 MET cc_start: 0.8740 (pmm) cc_final: 0.8484 (pmm) REVERT: d 415 MET cc_start: 0.8132 (mpp) cc_final: 0.7915 (ptp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1415 time to fit residues: 27.3531 Evaluate side-chains 108 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 175 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.029577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.023318 restraints weight = 348792.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.023899 restraints weight = 257661.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.024321 restraints weight = 206018.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.024629 restraints weight = 174105.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.024860 restraints weight = 153101.875| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20401 Z= 0.115 Angle : 0.594 7.818 27503 Z= 0.284 Chirality : 0.041 0.165 3135 Planarity : 0.004 0.053 3525 Dihedral : 9.968 169.410 2917 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % 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: 0.60 (0.17), residues: 2490 helix: 0.90 (0.15), residues: 1182 sheet: -0.69 (0.26), residues: 390 loop : 0.49 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 366 TYR 0.013 0.001 TYR f 332 PHE 0.011 0.001 PHE f 36 TRP 0.006 0.001 TRP d 381 HIS 0.006 0.001 HIS c 42 Details of bonding type rmsd covalent geometry : bond 0.00242 (20371) covalent geometry : angle 0.59431 (27503) hydrogen bonds : bond 0.02658 ( 944) hydrogen bonds : angle 4.23249 ( 2742) Misc. bond : bond 0.00329 ( 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 122 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0570 (ttt) cc_final: -0.1204 (ttt) REVERT: f 1 MET cc_start: 0.5783 (pmm) cc_final: 0.5481 (pmm) REVERT: f 219 MET cc_start: 0.9059 (mmp) cc_final: 0.8756 (mmm) REVERT: f 341 MET cc_start: 0.5517 (tmm) cc_final: 0.5135 (tmm) REVERT: f 396 MET cc_start: 0.9203 (mmp) cc_final: 0.8935 (mtp) REVERT: c 1 MET cc_start: 0.8670 (mtm) cc_final: 0.8375 (tpp) REVERT: c 147 MET cc_start: 0.6394 (tpt) cc_final: 0.5784 (mpp) REVERT: c 390 MET cc_start: 0.8864 (ptt) cc_final: 0.8421 (ptt) REVERT: b 8 ASN cc_start: 0.9334 (m-40) cc_final: 0.8937 (p0) REVERT: b 29 MET cc_start: 0.5029 (mtp) cc_final: 0.4736 (ttp) REVERT: b 111 PHE cc_start: 0.9107 (m-80) cc_final: 0.8532 (m-80) REVERT: b 147 MET cc_start: 0.8555 (mpp) cc_final: 0.7349 (tpt) REVERT: a 1 MET cc_start: 0.7586 (pmm) cc_final: 0.7374 (pmm) REVERT: a 72 TYR cc_start: 0.9044 (m-10) cc_final: 0.8778 (m-10) REVERT: a 147 MET cc_start: 0.7120 (tpt) cc_final: 0.6476 (mpp) REVERT: a 245 MET cc_start: 0.9269 (ptp) cc_final: 0.8251 (ptp) REVERT: a 248 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9143 (pt0) REVERT: a 396 MET cc_start: 0.8985 (mtt) cc_final: 0.8432 (mmm) REVERT: d 8 ASN cc_start: 0.9343 (m-40) cc_final: 0.9100 (p0) REVERT: d 21 MET cc_start: -0.1980 (mtp) cc_final: -0.2328 (ttp) REVERT: d 147 MET cc_start: 0.8505 (mmp) cc_final: 0.7744 (tpt) REVERT: d 390 MET cc_start: 0.8692 (pmm) cc_final: 0.8405 (pmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1304 time to fit residues: 25.7174 Evaluate side-chains 113 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 188 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 ASN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 292 ASN ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.027894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.021869 restraints weight = 362816.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.022432 restraints weight = 267596.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.022840 restraints weight = 213644.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.023137 restraints weight = 180317.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.023358 restraints weight = 158444.630| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.9158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20401 Z= 0.167 Angle : 0.670 8.193 27503 Z= 0.324 Chirality : 0.042 0.170 3135 Planarity : 0.004 0.060 3525 Dihedral : 10.118 169.778 2917 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2490 helix: 0.77 (0.14), residues: 1176 sheet: -0.81 (0.25), residues: 390 loop : 0.43 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG f 221 TYR 0.012 0.002 TYR d 332 PHE 0.013 0.002 PHE c 62 TRP 0.003 0.001 TRP f 381 HIS 0.006 0.001 HIS c 344 Details of bonding type rmsd covalent geometry : bond 0.00342 (20371) covalent geometry : angle 0.66986 (27503) hydrogen bonds : bond 0.03137 ( 944) hydrogen bonds : angle 4.47349 ( 2742) Misc. bond : bond 0.00377 ( 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 120 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0592 (ttt) cc_final: -0.1069 (ttt) REVERT: f 29 MET cc_start: 0.2568 (ttm) cc_final: 0.2209 (ptm) REVERT: f 207 LEU cc_start: 0.9379 (pt) cc_final: 0.9055 (tp) REVERT: f 219 MET cc_start: 0.9045 (mmp) cc_final: 0.8753 (mmp) REVERT: f 341 MET cc_start: 0.6250 (tmm) cc_final: 0.5945 (tmm) REVERT: f 396 MET cc_start: 0.9243 (mmp) cc_final: 0.8881 (mmm) REVERT: c 147 MET cc_start: 0.6395 (tpt) cc_final: 0.5802 (mpp) REVERT: c 390 MET cc_start: 0.8922 (ptt) cc_final: 0.8545 (ptt) REVERT: b 8 ASN cc_start: 0.9334 (m-40) cc_final: 0.8930 (p0) REVERT: b 29 MET cc_start: 0.5927 (mtp) cc_final: 0.5269 (mtp) REVERT: a 1 MET cc_start: 0.7602 (pmm) cc_final: 0.7345 (pmm) REVERT: a 147 MET cc_start: 0.7182 (tpt) cc_final: 0.6551 (mpp) REVERT: a 245 MET cc_start: 0.9365 (ptp) cc_final: 0.8155 (ptp) REVERT: a 248 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9208 (pt0) REVERT: a 327 MET cc_start: 0.9471 (tpt) cc_final: 0.9107 (mmm) REVERT: a 396 MET cc_start: 0.9082 (mtt) cc_final: 0.8636 (mmm) REVERT: d 8 ASN cc_start: 0.9413 (m-40) cc_final: 0.9163 (p0) REVERT: d 21 MET cc_start: -0.1185 (mtp) cc_final: -0.1555 (ttp) REVERT: d 29 MET cc_start: 0.8683 (ptt) cc_final: 0.8347 (ptp) REVERT: d 147 MET cc_start: 0.8485 (mmp) cc_final: 0.7718 (tpt) REVERT: d 390 MET cc_start: 0.8882 (pmm) cc_final: 0.8594 (pmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1418 time to fit residues: 26.8012 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 220 GLN a 20 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.027394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.021482 restraints weight = 364009.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.022042 restraints weight = 265865.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.022448 restraints weight = 211066.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.022737 restraints weight = 177771.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.022951 restraints weight = 155997.234| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.9756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20401 Z= 0.151 Angle : 0.642 9.501 27503 Z= 0.309 Chirality : 0.042 0.204 3135 Planarity : 0.004 0.044 3525 Dihedral : 9.941 167.979 2917 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.38 (0.17), residues: 2490 helix: 0.87 (0.15), residues: 1176 sheet: -1.12 (0.24), residues: 456 loop : 0.49 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 366 TYR 0.013 0.001 TYR d 332 PHE 0.011 0.001 PHE c 62 TRP 0.007 0.001 TRP b 381 HIS 0.010 0.001 HIS c 42 Details of bonding type rmsd covalent geometry : bond 0.00308 (20371) covalent geometry : angle 0.64191 (27503) hydrogen bonds : bond 0.03009 ( 944) hydrogen bonds : angle 4.44987 ( 2742) Misc. bond : bond 0.00343 ( 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 121 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.898 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: e 21 MET cc_start: -0.0265 (ttt) cc_final: -0.0485 (ttt) REVERT: f 207 LEU cc_start: 0.9417 (pt) cc_final: 0.9152 (tp) REVERT: f 219 MET cc_start: 0.8945 (mmp) cc_final: 0.8709 (mmp) REVERT: f 341 MET cc_start: 0.6716 (tmm) cc_final: 0.6426 (tmm) REVERT: f 396 MET cc_start: 0.9275 (mmp) cc_final: 0.8885 (mmm) REVERT: c 147 MET cc_start: 0.6555 (tpt) cc_final: 0.5985 (mpp) REVERT: c 390 MET cc_start: 0.9060 (ptt) cc_final: 0.8538 (ptt) REVERT: b 29 MET cc_start: 0.6096 (mtp) cc_final: 0.5426 (mtp) REVERT: b 111 PHE cc_start: 0.9153 (m-80) cc_final: 0.8636 (m-80) REVERT: b 396 MET cc_start: 0.8848 (mmm) cc_final: 0.8024 (mmp) REVERT: a 29 MET cc_start: 0.2882 (ptm) cc_final: 0.2590 (tmm) REVERT: a 147 MET cc_start: 0.7312 (tpt) cc_final: 0.6779 (mpp) REVERT: a 396 MET cc_start: 0.9123 (mtt) cc_final: 0.8753 (mmm) REVERT: d 21 MET cc_start: -0.1274 (mtp) cc_final: -0.1657 (ttp) REVERT: d 29 MET cc_start: 0.8497 (ptt) cc_final: 0.8249 (ptp) REVERT: d 147 MET cc_start: 0.8142 (mmp) cc_final: 0.7389 (tpt) REVERT: d 390 MET cc_start: 0.8902 (pmm) cc_final: 0.8608 (pmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1593 time to fit residues: 30.2890 Evaluate side-chains 108 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN e 292 ASN ** f 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 292 ASN c 25 ASN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 ASN c 189 GLN c 190 ASN ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.021916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.016611 restraints weight = 402473.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.016954 restraints weight = 330893.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.017219 restraints weight = 283040.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.017422 restraints weight = 250484.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.017583 restraints weight = 227555.253| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 1.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20401 Z= 0.249 Angle : 0.814 9.841 27503 Z= 0.405 Chirality : 0.046 0.196 3135 Planarity : 0.005 0.077 3525 Dihedral : 10.433 169.955 2917 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2490 helix: 0.22 (0.14), residues: 1176 sheet: -1.24 (0.25), residues: 378 loop : 0.16 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG e 102 TYR 0.018 0.003 TYR b 80 PHE 0.034 0.002 PHE b 335 TRP 0.006 0.001 TRP d 381 HIS 0.010 0.002 HIS c 344 Details of bonding type rmsd covalent geometry : bond 0.00506 (20371) covalent geometry : angle 0.81375 (27503) hydrogen bonds : bond 0.04239 ( 944) hydrogen bonds : angle 5.17279 ( 2742) Misc. bond : bond 0.00332 ( 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 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.877 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 21 MET cc_start: 0.1600 (ttt) cc_final: 0.1104 (ttt) REVERT: e 147 MET cc_start: 0.7609 (mpp) cc_final: 0.5174 (tpp) REVERT: e 207 LEU cc_start: 0.9643 (pt) cc_final: 0.9423 (pt) REVERT: f 29 MET cc_start: 0.3686 (ptm) cc_final: 0.2819 (tmm) REVERT: f 396 MET cc_start: 0.8929 (mmp) cc_final: 0.8606 (mmm) REVERT: c 29 MET cc_start: 0.2419 (ttt) cc_final: 0.1862 (ttt) REVERT: c 147 MET cc_start: 0.6301 (tpt) cc_final: 0.5919 (mpp) REVERT: b 29 MET cc_start: 0.7557 (mtp) cc_final: 0.6979 (mtm) REVERT: b 396 MET cc_start: 0.8926 (mmm) cc_final: 0.8212 (mmm) REVERT: a 147 MET cc_start: 0.7214 (tpt) cc_final: 0.6836 (mpp) REVERT: a 396 MET cc_start: 0.9017 (mtt) cc_final: 0.8661 (mmm) REVERT: d 147 MET cc_start: 0.8077 (mmp) cc_final: 0.7669 (mmp) REVERT: d 390 MET cc_start: 0.9138 (pmm) cc_final: 0.8926 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1597 time to fit residues: 29.2369 Evaluate side-chains 104 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 156 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 20 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 344 HIS ** d 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.027003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.021289 restraints weight = 362535.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.021860 restraints weight = 259661.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.022276 restraints weight = 203995.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.022579 restraints weight = 169922.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.022805 restraints weight = 147825.591| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 1.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20401 Z= 0.108 Angle : 0.627 8.576 27503 Z= 0.301 Chirality : 0.043 0.158 3135 Planarity : 0.004 0.045 3525 Dihedral : 9.858 169.633 2917 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2490 helix: 0.86 (0.15), residues: 1182 sheet: -1.12 (0.24), residues: 456 loop : 0.39 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 30 TYR 0.018 0.001 TYR a 332 PHE 0.028 0.001 PHE b 335 TRP 0.012 0.001 TRP b 381 HIS 0.009 0.001 HIS c 140 Details of bonding type rmsd covalent geometry : bond 0.00232 (20371) covalent geometry : angle 0.62693 (27503) hydrogen bonds : bond 0.02749 ( 944) hydrogen bonds : angle 4.50185 ( 2742) Misc. bond : bond 0.00318 ( 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 121 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.891 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 1 MET cc_start: 0.8708 (tpp) cc_final: 0.8098 (tpp) REVERT: e 21 MET cc_start: 0.0981 (ttt) cc_final: 0.0640 (ttt) REVERT: e 29 MET cc_start: 0.5781 (ttm) cc_final: 0.5380 (ttt) REVERT: e 147 MET cc_start: 0.7637 (mpp) cc_final: 0.5536 (tpp) REVERT: f 29 MET cc_start: 0.2092 (ptm) cc_final: 0.1884 (tmm) REVERT: f 341 MET cc_start: 0.8273 (tmm) cc_final: 0.8071 (tmm) REVERT: f 390 MET cc_start: 0.8427 (pmm) cc_final: 0.8100 (pmm) REVERT: f 396 MET cc_start: 0.9210 (mmp) cc_final: 0.8986 (mtp) REVERT: c 147 MET cc_start: 0.6485 (tpt) cc_final: 0.6054 (mpp) REVERT: c 327 MET cc_start: 0.7499 (ttt) cc_final: 0.6752 (tmm) REVERT: c 390 MET cc_start: 0.9138 (pmm) cc_final: 0.8646 (pmm) REVERT: b 29 MET cc_start: 0.7230 (mtp) cc_final: 0.6834 (mtp) REVERT: b 111 PHE cc_start: 0.9028 (m-80) cc_final: 0.8407 (m-80) REVERT: b 396 MET cc_start: 0.8921 (mmm) cc_final: 0.8304 (mmp) REVERT: a 1 MET cc_start: 0.7488 (pmm) cc_final: 0.6760 (ptp) REVERT: a 147 MET cc_start: 0.7471 (tpt) cc_final: 0.6994 (mpp) REVERT: a 390 MET cc_start: 0.8872 (ptp) cc_final: 0.8455 (ptt) REVERT: a 396 MET cc_start: 0.9088 (mtt) cc_final: 0.8646 (mmm) REVERT: d 21 MET cc_start: -0.1547 (mtp) cc_final: -0.1792 (ttp) REVERT: d 29 MET cc_start: 0.7698 (pmm) cc_final: 0.6219 (pmm) REVERT: d 147 MET cc_start: 0.7778 (mmp) cc_final: 0.7562 (mmp) REVERT: d 186 MET cc_start: 0.9345 (tmm) cc_final: 0.9133 (ppp) REVERT: d 390 MET cc_start: 0.8872 (pmm) cc_final: 0.8590 (pmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1615 time to fit residues: 30.7229 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 : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 49 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 226 optimal weight: 0.0670 chunk 210 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.3320 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 239 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.026730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.021013 restraints weight = 366898.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.021589 restraints weight = 264069.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.022003 restraints weight = 206992.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.022307 restraints weight = 172297.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.022533 restraints weight = 149651.004| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 1.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20401 Z= 0.105 Angle : 0.619 8.964 27503 Z= 0.296 Chirality : 0.042 0.146 3135 Planarity : 0.004 0.047 3525 Dihedral : 9.746 165.810 2917 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 0.53 (0.17), residues: 2490 helix: 1.03 (0.15), residues: 1182 sheet: -1.00 (0.24), residues: 462 loop : 0.46 (0.24), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 366 TYR 0.015 0.001 TYR d 332 PHE 0.023 0.001 PHE b 335 TRP 0.008 0.001 TRP b 381 HIS 0.006 0.001 HIS c 140 Details of bonding type rmsd covalent geometry : bond 0.00226 (20371) covalent geometry : angle 0.61936 (27503) hydrogen bonds : bond 0.02690 ( 944) hydrogen bonds : angle 4.43057 ( 2742) Misc. bond : bond 0.00299 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.88 seconds wall clock time: 61 minutes 45.33 seconds (3705.33 seconds total)