Starting phenix.real_space_refine on Tue Jun 17 20:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5p_27917/06_2025/8e5p_27917_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12524 2.51 5 N 3538 2.21 5 O 3824 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20038 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.17, per 1000 atoms: 0.66 Number of scatterers: 20038 At special positions: 0 Unit cell: (139.7, 116.6, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 20 15.00 Mg 6 11.99 F 18 9.00 O 3824 8.00 N 3538 7.00 C 12524 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.73 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.31 Creating SS restraints... Processing helix chain 'e' and resid 2 through 9 Processing helix chain 'e' and resid 10 through 22 Processing helix chain 'e' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 132 through 136 Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 338 removed outlier: 3.555A pdb=" N GLU e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 371 Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 391 through 404 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS e 417 " --> pdb=" O PHE e 413 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 Processing helix chain 'f' and resid 10 through 22 Processing helix chain 'f' and resid 30 through 45 removed outlier: 3.705A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 90 Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 132 through 136 Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 221 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 335 removed outlier: 3.717A pdb=" N GLU f 329 " --> pdb=" O SER f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 371 Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 391 through 404 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.717A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS f 417 " --> pdb=" O PHE f 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 Processing helix chain 'c' and resid 10 through 22 Processing helix chain 'c' and resid 30 through 45 removed outlier: 3.700A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 90 Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 221 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU c 333 " --> pdb=" O GLU c 329 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 371 Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 391 through 404 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS c 417 " --> pdb=" O PHE c 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 Processing helix chain 'b' and resid 10 through 22 Processing helix chain 'b' and resid 30 through 45 removed outlier: 3.704A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 90 Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 132 through 136 Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 221 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.596A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 335 removed outlier: 3.643A pdb=" N GLU b 333 " --> pdb=" O GLU b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 391 through 404 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.722A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS b 417 " --> pdb=" O PHE b 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 10 through 22 Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 90 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 132 through 136 Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 221 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 337 removed outlier: 4.202A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 371 Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 391 through 404 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS a 417 " --> pdb=" O PHE a 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 Processing helix chain 'd' and resid 10 through 22 Processing helix chain 'd' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 90 Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.266A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 221 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 333 Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 371 Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 391 through 404 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR e 96 " --> pdb=" O VAL e 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL e 119 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER e 98 " --> pdb=" O ASN e 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS e 115 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG e 102 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN e 306 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA e 317 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU e 342 " --> pdb=" O GLY e 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY e 364 " --> pdb=" O GLU e 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR f 96 " --> pdb=" O VAL f 119 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL f 119 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER f 98 " --> pdb=" O ASN f 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS f 115 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG f 102 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU f 113 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.805A pdb=" N ASN f 306 " --> pdb=" O LEU f 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.479A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA f 317 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU f 342 " --> pdb=" O GLY f 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY f 364 " --> pdb=" O GLU f 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 63 through 66 removed outlier: 3.851A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR c 96 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL c 119 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER c 98 " --> pdb=" O ASN c 117 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS c 115 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG c 102 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN c 306 " --> pdb=" O LEU c 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA c 317 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU c 342 " --> pdb=" O GLY c 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY c 364 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 63 through 66 removed outlier: 3.855A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR b 96 " --> pdb=" O VAL b 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 119 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 98 " --> pdb=" O ASN b 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS b 115 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG b 102 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU b 113 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN b 306 " --> pdb=" O LEU b 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.476A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA b 317 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU b 342 " --> pdb=" O GLY b 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY b 364 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'a' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR a 96 " --> pdb=" O VAL a 119 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL a 119 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER a 98 " --> pdb=" O ASN a 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS a 115 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG a 102 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN a 306 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA a 317 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU a 342 " --> pdb=" O GLY a 364 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY a 364 " --> pdb=" O GLU a 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR d 96 " --> pdb=" O VAL d 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL d 119 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER d 98 " --> pdb=" O ASN d 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS d 115 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG d 102 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU d 113 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.806A pdb=" N ASN d 306 " --> pdb=" O LEU d 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA d 317 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 364 " --> pdb=" O GLU d 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 944 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4633 1.33 - 1.45: 3721 1.45 - 1.57: 11764 1.57 - 1.69: 33 1.69 - 1.81: 198 Bond restraints: 20349 Sorted by residual: bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.564 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" F2 BEF f1002 " pdb="BE BEF f1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 20344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 27254 2.89 - 5.77: 166 5.77 - 8.66: 37 8.66 - 11.54: 6 11.54 - 14.43: 6 Bond angle restraints: 27469 Sorted by residual: angle pdb=" N ASP f 322 " pdb=" CA ASP f 322 " pdb=" C ASP f 322 " ideal model delta sigma weight residual 112.58 105.29 7.29 1.22e+00 6.72e-01 3.57e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.74 6.59 1.21e+00 6.83e-01 2.97e+01 angle pdb=" N GLU c 334 " pdb=" CA GLU c 334 " pdb=" C GLU c 334 " ideal model delta sigma weight residual 111.33 105.03 6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " pdb=" F3 BEF e1002 " ideal model delta sigma weight residual 119.96 105.53 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.54 14.42 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 12388 29.83 - 59.65: 147 59.65 - 89.48: 48 89.48 - 119.31: 2 119.31 - 149.14: 6 Dihedral angle restraints: 12591 sinusoidal: 5397 harmonic: 7194 Sorted by residual: dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.13 -149.14 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP c1000 " pdb=" O3A ADP c1000 " pdb=" PB ADP c1000 " pdb=" PA ADP c1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.09 -149.10 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PA ADP d1000 " pdb=" PB ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 84.35 -144.35 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2607 0.052 - 0.104: 406 0.104 - 0.155: 109 0.155 - 0.207: 7 0.207 - 0.259: 1 Chirality restraints: 3130 Sorted by residual: chirality pdb=" C3' A 7 1 " pdb=" C4' A 7 1 " pdb=" O3' A 7 1 " pdb=" C2' A 7 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL d 330 " pdb=" N VAL d 330 " pdb=" C VAL d 330 " pdb=" CB VAL d 330 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C3' U 7 2 " pdb=" C4' U 7 2 " pdb=" O3' U 7 2 " pdb=" C2' U 7 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 3127 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C ILE b 331 " -0.112 2.00e-02 2.50e+03 pdb=" O ILE b 331 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR b 332 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 331 " -0.028 2.00e-02 2.50e+03 5.66e-02 3.20e+01 pdb=" C ILE e 331 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE e 331 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR e 332 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 331 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ILE c 331 " -0.086 2.00e-02 2.50e+03 pdb=" O ILE c 331 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR c 332 " 0.028 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 55 2.02 - 2.74: 1636 2.74 - 3.46: 29031 3.46 - 4.18: 46224 4.18 - 4.90: 83568 Nonbonded interactions: 160514 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 3.040 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 nonbonded pdb=" NH1 ARG e 272 " pdb=" OE2 GLU f 334 " model vdw 1.417 3.120 nonbonded pdb=" NZ LYS e 385 " pdb=" O LYS d 352 " model vdw 1.494 3.120 ... (remaining 160509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 48.680 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.748 20379 Z= 1.844 Angle : 0.641 14.431 27469 Z= 0.351 Chirality : 0.041 0.259 3130 Planarity : 0.004 0.065 3524 Dihedral : 11.506 149.136 7935 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 4.11 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP a 381 HIS 0.002 0.000 HIS e 295 PHE 0.007 0.001 PHE b 36 TYR 0.017 0.001 TYR d 332 ARG 0.003 0.000 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.19911 ( 944) hydrogen bonds : angle 6.53604 ( 2742) covalent geometry : bond 0.00344 (20349) covalent geometry : angle 0.64136 (27469) Misc. bond : bond 0.47742 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.2762 (mmm) cc_final: 0.1608 (ttt) REVERT: c 29 MET cc_start: -0.3216 (mtp) cc_final: -0.3709 (ttt) REVERT: c 341 MET cc_start: -0.1671 (ttm) cc_final: -0.1952 (tmm) outliers start: 35 outliers final: 9 residues processed: 198 average time/residue: 0.3183 time to fit residues: 97.8280 Evaluate side-chains 126 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 193 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 172 GLN e 256 HIS ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 ASN ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS b 135 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 HIS a 135 ASN a 172 GLN ** a 189 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 = 0.3715 r_free = 0.3715 target = 0.039207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.031852 restraints weight = 352062.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.032083 restraints weight = 324613.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.032226 restraints weight = 304465.040| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20379 Z= 0.257 Angle : 0.842 8.943 27469 Z= 0.411 Chirality : 0.046 0.275 3130 Planarity : 0.006 0.124 3524 Dihedral : 10.570 163.903 2901 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2490 helix: 0.49 (0.15), residues: 1110 sheet: -0.90 (0.26), residues: 384 loop : -0.00 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 381 HIS 0.009 0.002 HIS a 388 PHE 0.027 0.002 PHE b 335 TYR 0.026 0.003 TYR d 332 ARG 0.009 0.001 ARG f 212 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 944) hydrogen bonds : angle 4.70401 ( 2742) covalent geometry : bond 0.00519 (20349) covalent geometry : angle 0.84237 (27469) Misc. bond : bond 0.00333 ( 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 113 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 380 MET cc_start: 0.9592 (mmm) cc_final: 0.9307 (mmm) REVERT: e 390 MET cc_start: 0.7987 (ptp) cc_final: 0.7187 (ptt) REVERT: f 21 MET cc_start: 0.1061 (mmm) cc_final: 0.0536 (mtt) REVERT: f 29 MET cc_start: 0.2461 (mtp) cc_final: 0.1471 (ttm) REVERT: f 147 MET cc_start: 0.8477 (mmp) cc_final: 0.7645 (mpp) REVERT: f 219 MET cc_start: 0.9456 (mmp) cc_final: 0.9235 (mmm) REVERT: f 380 MET cc_start: 0.9305 (tmm) cc_final: 0.9090 (tmm) REVERT: f 396 MET cc_start: 0.9314 (mmp) cc_final: 0.9085 (mmp) REVERT: c 21 MET cc_start: 0.5895 (mmm) cc_final: 0.5496 (ttp) REVERT: c 29 MET cc_start: 0.0425 (mtp) cc_final: -0.0047 (ttt) REVERT: c 341 MET cc_start: -0.1195 (ttm) cc_final: -0.2009 (tmm) REVERT: b 147 MET cc_start: 0.7662 (mmm) cc_final: 0.7326 (mpp) REVERT: b 205 MET cc_start: 0.8082 (tpt) cc_final: 0.7872 (tpt) REVERT: b 248 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9148 (mm-30) REVERT: b 396 MET cc_start: 0.8171 (mtp) cc_final: 0.7521 (mtp) REVERT: a 219 MET cc_start: 0.9422 (mmp) cc_final: 0.8903 (mmm) REVERT: a 380 MET cc_start: 0.9483 (mmp) cc_final: 0.9256 (mmm) REVERT: a 390 MET cc_start: 0.7471 (pmm) cc_final: 0.6795 (pmm) REVERT: a 396 MET cc_start: 0.9203 (mtp) cc_final: 0.8638 (ttm) REVERT: d 147 MET cc_start: 0.9461 (tpp) cc_final: 0.9199 (tpp) REVERT: d 416 MET cc_start: 0.5200 (ptt) cc_final: 0.4967 (ptt) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.3115 time to fit residues: 57.7563 Evaluate side-chains 101 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 38 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** f 25 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.037645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.030426 restraints weight = 356528.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.030655 restraints weight = 329488.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.030949 restraints weight = 307712.359| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20379 Z= 0.169 Angle : 0.658 7.216 27469 Z= 0.320 Chirality : 0.042 0.154 3130 Planarity : 0.004 0.045 3524 Dihedral : 10.183 165.059 2901 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2490 helix: 0.63 (0.15), residues: 1164 sheet: -0.56 (0.26), residues: 408 loop : 0.23 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 381 HIS 0.005 0.001 HIS f 344 PHE 0.011 0.001 PHE f 301 TYR 0.019 0.001 TYR d 332 ARG 0.008 0.001 ARG d 173 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 944) hydrogen bonds : angle 4.24271 ( 2742) covalent geometry : bond 0.00350 (20349) covalent geometry : angle 0.65846 (27469) Misc. bond : bond 0.00282 ( 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 105 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 380 MET cc_start: 0.9562 (mmm) cc_final: 0.9330 (mmm) REVERT: f 21 MET cc_start: 0.1350 (mmm) cc_final: 0.0777 (mtt) REVERT: f 29 MET cc_start: 0.1707 (mtp) cc_final: 0.1208 (ttm) REVERT: f 186 MET cc_start: 0.9152 (tmm) cc_final: 0.8804 (tmm) REVERT: f 219 MET cc_start: 0.9304 (mmp) cc_final: 0.9095 (mmm) REVERT: f 396 MET cc_start: 0.9314 (mmp) cc_final: 0.9010 (mmp) REVERT: c 29 MET cc_start: 0.0161 (mtp) cc_final: -0.0389 (ttt) REVERT: c 341 MET cc_start: -0.1682 (ttm) cc_final: -0.2435 (tmm) REVERT: c 390 MET cc_start: 0.5543 (pmm) cc_final: 0.5272 (pmm) REVERT: b 21 MET cc_start: 0.4014 (ttt) cc_final: 0.3151 (ttt) REVERT: b 147 MET cc_start: 0.7362 (mmm) cc_final: 0.6635 (mpp) REVERT: b 248 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9224 (mm-30) REVERT: b 341 MET cc_start: -0.0640 (mtm) cc_final: -0.0869 (mtm) REVERT: b 390 MET cc_start: 0.4755 (ptt) cc_final: 0.3871 (ptt) REVERT: b 396 MET cc_start: 0.8331 (mtp) cc_final: 0.7681 (mtp) REVERT: a 29 MET cc_start: -0.0884 (ttm) cc_final: -0.1721 (ttm) REVERT: a 219 MET cc_start: 0.9293 (mmp) cc_final: 0.8859 (mmm) REVERT: a 390 MET cc_start: 0.7274 (pmm) cc_final: 0.6803 (pmm) REVERT: d 8 ASN cc_start: 0.9650 (m-40) cc_final: 0.9391 (p0) REVERT: d 147 MET cc_start: 0.9494 (tpp) cc_final: 0.9098 (tpt) REVERT: d 390 MET cc_start: 0.6897 (ptp) cc_final: 0.6177 (ptt) REVERT: d 396 MET cc_start: 0.9378 (mtp) cc_final: 0.8866 (mtp) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.3038 time to fit residues: 52.7514 Evaluate side-chains 103 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 21 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** f 189 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.037937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.030729 restraints weight = 356137.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.030989 restraints weight = 326273.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 12)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.031155 restraints weight = 302517.332| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20379 Z= 0.095 Angle : 0.559 8.884 27469 Z= 0.266 Chirality : 0.041 0.129 3130 Planarity : 0.003 0.044 3524 Dihedral : 9.891 165.094 2901 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2490 helix: 1.14 (0.15), residues: 1158 sheet: -0.35 (0.26), residues: 408 loop : 0.49 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 381 HIS 0.004 0.001 HIS f 344 PHE 0.009 0.001 PHE f 301 TYR 0.018 0.001 TYR d 332 ARG 0.005 0.000 ARG d 173 Details of bonding type rmsd hydrogen bonds : bond 0.02522 ( 944) hydrogen bonds : angle 3.93440 ( 2742) covalent geometry : bond 0.00197 (20349) covalent geometry : angle 0.55854 (27469) Misc. bond : bond 0.00240 ( 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 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0260 (ttt) cc_final: -0.0476 (ttt) REVERT: e 380 MET cc_start: 0.9548 (mmm) cc_final: 0.9315 (mmm) REVERT: e 390 MET cc_start: 0.7955 (ptp) cc_final: 0.7311 (ptt) REVERT: e 396 MET cc_start: 0.9274 (ppp) cc_final: 0.8956 (ppp) REVERT: f 21 MET cc_start: 0.1355 (mmm) cc_final: 0.0634 (mtt) REVERT: f 147 MET cc_start: 0.8250 (mmp) cc_final: 0.7441 (mpp) REVERT: f 186 MET cc_start: 0.9091 (tmm) cc_final: 0.8815 (tmm) REVERT: f 219 MET cc_start: 0.9236 (mmp) cc_final: 0.8915 (mmt) REVERT: f 396 MET cc_start: 0.9324 (mmp) cc_final: 0.8979 (mmp) REVERT: c 21 MET cc_start: 0.4586 (mmp) cc_final: 0.3975 (ptm) REVERT: c 341 MET cc_start: -0.1790 (ttm) cc_final: -0.2635 (tmm) REVERT: c 390 MET cc_start: 0.6258 (pmm) cc_final: 0.5813 (pmm) REVERT: b 21 MET cc_start: 0.3916 (ttt) cc_final: 0.3047 (ttt) REVERT: b 29 MET cc_start: 0.1264 (ttt) cc_final: 0.1057 (ttt) REVERT: b 390 MET cc_start: 0.4474 (ptt) cc_final: 0.3702 (ptt) REVERT: a 219 MET cc_start: 0.9081 (mmp) cc_final: 0.8652 (mmm) REVERT: a 390 MET cc_start: 0.7086 (pmm) cc_final: 0.6637 (pmm) REVERT: a 396 MET cc_start: 0.9300 (ttm) cc_final: 0.8977 (ptt) REVERT: d 8 ASN cc_start: 0.9674 (m-40) cc_final: 0.9443 (p0) REVERT: d 29 MET cc_start: 0.1835 (ttt) cc_final: 0.1609 (ttt) REVERT: d 147 MET cc_start: 0.9491 (tpp) cc_final: 0.9272 (tpp) REVERT: d 390 MET cc_start: 0.6687 (ptp) cc_final: 0.5874 (ptt) REVERT: d 396 MET cc_start: 0.9312 (mtp) cc_final: 0.8699 (mtp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2959 time to fit residues: 52.5247 Evaluate side-chains 103 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 58 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.036488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.029436 restraints weight = 362300.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.029710 restraints weight = 331984.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.029877 restraints weight = 306725.225| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20379 Z= 0.120 Angle : 0.580 7.746 27469 Z= 0.277 Chirality : 0.041 0.130 3130 Planarity : 0.003 0.034 3524 Dihedral : 9.827 162.669 2901 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2490 helix: 1.24 (0.15), residues: 1158 sheet: -0.26 (0.26), residues: 408 loop : 0.62 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP a 381 HIS 0.005 0.001 HIS f 344 PHE 0.015 0.001 PHE f 121 TYR 0.017 0.001 TYR a 332 ARG 0.003 0.000 ARG f 173 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 944) hydrogen bonds : angle 3.87564 ( 2742) covalent geometry : bond 0.00257 (20349) covalent geometry : angle 0.58003 (27469) Misc. bond : bond 0.00209 ( 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 106 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0020 (ttt) cc_final: -0.0271 (ttt) REVERT: e 380 MET cc_start: 0.9614 (mmm) cc_final: 0.9327 (mmm) REVERT: e 396 MET cc_start: 0.9332 (ppp) cc_final: 0.8994 (ppp) REVERT: f 21 MET cc_start: 0.1486 (mmm) cc_final: 0.0785 (mtt) REVERT: f 29 MET cc_start: 0.1357 (mtp) cc_final: 0.0460 (ttp) REVERT: f 245 MET cc_start: 0.8509 (ptp) cc_final: 0.8280 (ptp) REVERT: f 396 MET cc_start: 0.9295 (mmp) cc_final: 0.8996 (mmp) REVERT: c 341 MET cc_start: -0.1574 (ttm) cc_final: -0.2458 (tmm) REVERT: c 390 MET cc_start: 0.6331 (pmm) cc_final: 0.5874 (pmm) REVERT: b 21 MET cc_start: 0.3681 (ttt) cc_final: 0.2650 (ttt) REVERT: b 248 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9194 (mm-30) REVERT: b 390 MET cc_start: 0.4922 (ptt) cc_final: 0.4049 (ptt) REVERT: b 396 MET cc_start: 0.8365 (mtp) cc_final: 0.7625 (mtp) REVERT: a 1 MET cc_start: 0.7591 (pmm) cc_final: 0.7218 (pmm) REVERT: a 219 MET cc_start: 0.9055 (mmp) cc_final: 0.8659 (mmm) REVERT: a 390 MET cc_start: 0.7027 (pmm) cc_final: 0.6731 (pmm) REVERT: a 396 MET cc_start: 0.9300 (ttm) cc_final: 0.8988 (ptt) REVERT: d 341 MET cc_start: -0.1757 (mmt) cc_final: -0.2327 (mmt) REVERT: d 390 MET cc_start: 0.6897 (ptp) cc_final: 0.6060 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2919 time to fit residues: 51.6692 Evaluate side-chains 100 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 96 optimal weight: 0.0470 chunk 192 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 197 optimal weight: 0.0010 chunk 77 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 177 optimal weight: 0.4980 chunk 188 optimal weight: 0.0170 chunk 122 optimal weight: 0.1980 chunk 22 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 32 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.037098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.030041 restraints weight = 356772.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.030238 restraints weight = 323381.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.030442 restraints weight = 301610.786| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20379 Z= 0.097 Angle : 0.577 8.074 27469 Z= 0.268 Chirality : 0.042 0.251 3130 Planarity : 0.003 0.049 3524 Dihedral : 9.738 162.658 2901 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2490 helix: 1.39 (0.15), residues: 1158 sheet: -0.21 (0.26), residues: 408 loop : 0.68 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 381 HIS 0.003 0.001 HIS f 344 PHE 0.012 0.001 PHE f 121 TYR 0.018 0.001 TYR f 332 ARG 0.007 0.000 ARG c 366 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 944) hydrogen bonds : angle 3.79394 ( 2742) covalent geometry : bond 0.00199 (20349) covalent geometry : angle 0.57697 (27469) Misc. bond : bond 0.00385 ( 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 108 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0592 (ttt) cc_final: -0.0910 (ttt) REVERT: e 380 MET cc_start: 0.9583 (mmm) cc_final: 0.9311 (mmm) REVERT: e 390 MET cc_start: 0.8072 (pmm) cc_final: 0.7621 (pmm) REVERT: e 396 MET cc_start: 0.9312 (ppp) cc_final: 0.8959 (ppp) REVERT: f 21 MET cc_start: 0.1619 (mmm) cc_final: 0.0875 (mtt) REVERT: f 29 MET cc_start: 0.1367 (mtp) cc_final: 0.0426 (ttp) REVERT: f 219 MET cc_start: 0.9171 (mmp) cc_final: 0.8956 (mmm) REVERT: f 396 MET cc_start: 0.9326 (mmp) cc_final: 0.8987 (mmp) REVERT: c 1 MET cc_start: 0.8512 (pmm) cc_final: 0.8278 (pmm) REVERT: c 21 MET cc_start: 0.4459 (mmp) cc_final: 0.3895 (ptm) REVERT: c 341 MET cc_start: -0.1880 (ttm) cc_final: -0.2588 (tmm) REVERT: c 390 MET cc_start: 0.6613 (pmm) cc_final: 0.6124 (pmm) REVERT: b 21 MET cc_start: 0.3757 (ttt) cc_final: 0.2846 (ttt) REVERT: b 29 MET cc_start: 0.1929 (ttt) cc_final: 0.1693 (ttt) REVERT: b 390 MET cc_start: 0.4563 (ptt) cc_final: 0.3697 (ptt) REVERT: b 396 MET cc_start: 0.8382 (mtp) cc_final: 0.7633 (mtp) REVERT: a 219 MET cc_start: 0.8902 (mmp) cc_final: 0.8511 (mmm) REVERT: a 390 MET cc_start: 0.6668 (pmm) cc_final: 0.6364 (pmm) REVERT: a 396 MET cc_start: 0.9325 (ttm) cc_final: 0.9036 (ptt) REVERT: d 8 ASN cc_start: 0.9682 (m-40) cc_final: 0.9472 (p0) REVERT: d 147 MET cc_start: 0.8671 (tpt) cc_final: 0.7948 (tpt) REVERT: d 341 MET cc_start: -0.1859 (mmt) cc_final: -0.2422 (mmt) REVERT: d 390 MET cc_start: 0.6758 (ptp) cc_final: 0.5912 (ptt) REVERT: d 396 MET cc_start: 0.9391 (mtp) cc_final: 0.9025 (mtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2929 time to fit residues: 52.3355 Evaluate side-chains 102 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 231 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 126 ASN e 172 GLN f 42 HIS f 239 HIS ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 256 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.034262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.027543 restraints weight = 367841.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.027771 restraints weight = 332414.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.027896 restraints weight = 309268.718| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20379 Z= 0.164 Angle : 0.667 8.485 27469 Z= 0.320 Chirality : 0.042 0.140 3130 Planarity : 0.004 0.039 3524 Dihedral : 9.909 164.390 2901 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2490 helix: 1.13 (0.15), residues: 1158 sheet: -0.11 (0.27), residues: 378 loop : 0.56 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 381 HIS 0.005 0.001 HIS f 344 PHE 0.015 0.002 PHE d 413 TYR 0.031 0.002 TYR d 72 ARG 0.007 0.001 ARG f 221 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 944) hydrogen bonds : angle 3.99678 ( 2742) covalent geometry : bond 0.00344 (20349) covalent geometry : angle 0.66670 (27469) Misc. bond : bond 0.00343 ( 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 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0432 (ttt) cc_final: -0.0744 (ttt) REVERT: e 380 MET cc_start: 0.9631 (mmm) cc_final: 0.9170 (tmm) REVERT: e 390 MET cc_start: 0.8176 (pmm) cc_final: 0.7873 (pmm) REVERT: e 396 MET cc_start: 0.9328 (ppp) cc_final: 0.8979 (ppp) REVERT: f 21 MET cc_start: 0.1847 (mmm) cc_final: 0.1157 (mtt) REVERT: f 29 MET cc_start: 0.2279 (mtp) cc_final: 0.1670 (ttp) REVERT: f 147 MET cc_start: 0.8465 (mmp) cc_final: 0.7258 (mpp) REVERT: f 396 MET cc_start: 0.9277 (mmp) cc_final: 0.8796 (mtp) REVERT: c 147 MET cc_start: 0.7678 (tpt) cc_final: 0.6763 (mpp) REVERT: c 341 MET cc_start: -0.0905 (ttm) cc_final: -0.2089 (tmm) REVERT: c 390 MET cc_start: 0.6899 (pmm) cc_final: 0.6441 (pmm) REVERT: b 147 MET cc_start: 0.5687 (tpt) cc_final: 0.5296 (tpt) REVERT: b 390 MET cc_start: 0.5675 (ptt) cc_final: 0.4690 (ptt) REVERT: b 396 MET cc_start: 0.8569 (mtp) cc_final: 0.7757 (mtp) REVERT: a 147 MET cc_start: 0.7234 (tpt) cc_final: 0.6683 (mpp) REVERT: a 219 MET cc_start: 0.9111 (mmp) cc_final: 0.8763 (mmm) REVERT: a 390 MET cc_start: 0.6953 (pmm) cc_final: 0.6540 (pmm) REVERT: a 396 MET cc_start: 0.9419 (ttm) cc_final: 0.9060 (ptt) REVERT: d 147 MET cc_start: 0.8798 (tpt) cc_final: 0.7975 (tpt) REVERT: d 341 MET cc_start: -0.1142 (mmt) cc_final: -0.1773 (mmp) REVERT: d 390 MET cc_start: 0.7074 (ptp) cc_final: 0.6205 (ptt) REVERT: d 416 MET cc_start: 0.5798 (ptt) cc_final: 0.5593 (ptt) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.2849 time to fit residues: 50.2852 Evaluate side-chains 101 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 126 ASN ** f 241 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** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.033258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.026564 restraints weight = 378943.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.026841 restraints weight = 340790.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.027028 restraints weight = 311733.511| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20379 Z= 0.157 Angle : 0.649 8.702 27469 Z= 0.315 Chirality : 0.043 0.290 3130 Planarity : 0.004 0.093 3524 Dihedral : 9.856 161.447 2901 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2490 helix: 1.05 (0.15), residues: 1164 sheet: -0.13 (0.27), residues: 372 loop : 0.56 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 381 HIS 0.005 0.001 HIS f 344 PHE 0.016 0.002 PHE d 413 TYR 0.018 0.001 TYR d 332 ARG 0.017 0.001 ARG b 252 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 944) hydrogen bonds : angle 4.15069 ( 2742) covalent geometry : bond 0.00330 (20349) covalent geometry : angle 0.64931 (27469) Misc. bond : bond 0.00283 ( 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 107 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.329 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: e 21 MET cc_start: -0.1197 (ttt) cc_final: -0.1567 (ttt) REVERT: e 380 MET cc_start: 0.9608 (mmm) cc_final: 0.9396 (mmm) REVERT: e 390 MET cc_start: 0.8348 (pmm) cc_final: 0.7862 (pmm) REVERT: e 396 MET cc_start: 0.9322 (ppp) cc_final: 0.8937 (ppp) REVERT: f 21 MET cc_start: 0.2832 (mmm) cc_final: 0.2236 (mtt) REVERT: f 29 MET cc_start: 0.2101 (mtp) cc_final: 0.1378 (ttp) REVERT: f 219 MET cc_start: 0.9315 (mmp) cc_final: 0.9094 (mmm) REVERT: f 396 MET cc_start: 0.9307 (mmp) cc_final: 0.9072 (ttm) REVERT: c 1 MET cc_start: 0.6833 (ptt) cc_final: 0.6196 (ptt) REVERT: c 147 MET cc_start: 0.7409 (tpt) cc_final: 0.6580 (mpp) REVERT: c 341 MET cc_start: -0.0686 (ttm) cc_final: -0.1810 (tmm) REVERT: c 390 MET cc_start: 0.7076 (pmm) cc_final: 0.6601 (pmm) REVERT: b 21 MET cc_start: 0.4131 (ttt) cc_final: 0.3572 (ttm) REVERT: b 29 MET cc_start: 0.2192 (ttt) cc_final: 0.1161 (tmm) REVERT: b 245 MET cc_start: 0.8921 (ptp) cc_final: 0.8653 (ptt) REVERT: b 390 MET cc_start: 0.6150 (ptt) cc_final: 0.4992 (ptt) REVERT: b 396 MET cc_start: 0.8764 (mtp) cc_final: 0.8061 (mtp) REVERT: a 1 MET cc_start: 0.7368 (ptp) cc_final: 0.7088 (ptp) REVERT: a 219 MET cc_start: 0.9136 (mmp) cc_final: 0.8827 (mmm) REVERT: a 390 MET cc_start: 0.7224 (pmm) cc_final: 0.6827 (pmm) REVERT: d 29 MET cc_start: 0.2361 (ptm) cc_final: 0.2041 (tmm) REVERT: d 147 MET cc_start: 0.8742 (tpt) cc_final: 0.7971 (tpt) REVERT: d 390 MET cc_start: 0.6976 (ptp) cc_final: 0.6179 (ptt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2941 time to fit residues: 52.1612 Evaluate side-chains 98 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.032322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.025765 restraints weight = 382453.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.026031 restraints weight = 343299.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.026230 restraints weight = 314516.593| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20379 Z= 0.153 Angle : 0.652 10.102 27469 Z= 0.314 Chirality : 0.043 0.196 3130 Planarity : 0.004 0.036 3524 Dihedral : 9.908 163.269 2901 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2490 helix: 1.12 (0.15), residues: 1158 sheet: -0.19 (0.27), residues: 372 loop : 0.48 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP a 381 HIS 0.007 0.001 HIS b 344 PHE 0.010 0.001 PHE d 413 TYR 0.018 0.001 TYR b 332 ARG 0.010 0.001 ARG b 252 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 944) hydrogen bonds : angle 4.14288 ( 2742) covalent geometry : bond 0.00325 (20349) covalent geometry : angle 0.65220 (27469) Misc. bond : bond 0.00278 ( 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 105 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.1196 (ttt) cc_final: -0.1680 (ttt) REVERT: e 380 MET cc_start: 0.9586 (mmm) cc_final: 0.9377 (mmm) REVERT: e 390 MET cc_start: 0.8365 (pmm) cc_final: 0.8071 (pmm) REVERT: e 396 MET cc_start: 0.9321 (ppp) cc_final: 0.8917 (ppp) REVERT: f 29 MET cc_start: 0.2040 (mtp) cc_final: 0.1269 (ttp) REVERT: f 219 MET cc_start: 0.9361 (mmp) cc_final: 0.9110 (mmm) REVERT: f 390 MET cc_start: 0.8438 (ptt) cc_final: 0.7442 (ppp) REVERT: f 396 MET cc_start: 0.9297 (mmp) cc_final: 0.9077 (ttm) REVERT: c 1 MET cc_start: 0.7220 (ptt) cc_final: 0.6510 (ptt) REVERT: c 147 MET cc_start: 0.7461 (tpt) cc_final: 0.6625 (mpp) REVERT: c 341 MET cc_start: -0.0496 (ttm) cc_final: -0.1679 (tmm) REVERT: c 390 MET cc_start: 0.7220 (pmm) cc_final: 0.6743 (pmm) REVERT: c 396 MET cc_start: 0.9612 (ttm) cc_final: 0.9235 (ptt) REVERT: b 21 MET cc_start: 0.4097 (ttt) cc_final: 0.3495 (ttm) REVERT: b 29 MET cc_start: 0.2455 (ttt) cc_final: 0.1357 (tmm) REVERT: b 396 MET cc_start: 0.8866 (mtp) cc_final: 0.8165 (mtp) REVERT: a 1 MET cc_start: 0.7129 (ptp) cc_final: 0.6639 (ptp) REVERT: a 219 MET cc_start: 0.9175 (mmp) cc_final: 0.8845 (mmm) REVERT: a 390 MET cc_start: 0.7393 (pmm) cc_final: 0.7021 (pmm) REVERT: d 29 MET cc_start: 0.2849 (ptm) cc_final: 0.2571 (tmm) REVERT: d 147 MET cc_start: 0.8581 (tpt) cc_final: 0.7743 (tpt) REVERT: d 390 MET cc_start: 0.7112 (ptp) cc_final: 0.6294 (ptt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3069 time to fit residues: 52.7005 Evaluate side-chains 99 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 66 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.032250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.025811 restraints weight = 376030.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.026063 restraints weight = 333483.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.026240 restraints weight = 305242.954| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20379 Z= 0.107 Angle : 0.605 9.290 27469 Z= 0.288 Chirality : 0.042 0.164 3130 Planarity : 0.003 0.040 3524 Dihedral : 9.764 162.479 2901 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2490 helix: 1.33 (0.16), residues: 1152 sheet: -0.13 (0.27), residues: 372 loop : 0.54 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP b 381 HIS 0.005 0.001 HIS f 344 PHE 0.008 0.001 PHE f 301 TYR 0.029 0.001 TYR d 72 ARG 0.008 0.000 ARG b 252 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 944) hydrogen bonds : angle 4.06592 ( 2742) covalent geometry : bond 0.00229 (20349) covalent geometry : angle 0.60537 (27469) Misc. bond : bond 0.00263 ( 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 105 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.360 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: -0.1057 (ttt) cc_final: -0.1629 (ttt) REVERT: e 380 MET cc_start: 0.9559 (mmm) cc_final: 0.9351 (mmm) REVERT: e 390 MET cc_start: 0.8444 (pmm) cc_final: 0.7930 (pmm) REVERT: e 396 MET cc_start: 0.9277 (ppp) cc_final: 0.8863 (ppp) REVERT: f 29 MET cc_start: 0.2106 (mtp) cc_final: 0.1387 (ttp) REVERT: f 219 MET cc_start: 0.9255 (mmp) cc_final: 0.8995 (mmm) REVERT: f 390 MET cc_start: 0.8256 (ptt) cc_final: 0.7158 (ppp) REVERT: c 341 MET cc_start: -0.0500 (ttm) cc_final: -0.1512 (tmm) REVERT: c 390 MET cc_start: 0.6764 (pmm) cc_final: 0.6433 (pmm) REVERT: c 396 MET cc_start: 0.9603 (ttm) cc_final: 0.9235 (ptt) REVERT: b 1 MET cc_start: 0.8891 (pmm) cc_final: 0.8633 (ptp) REVERT: b 21 MET cc_start: 0.4055 (ttt) cc_final: 0.3431 (ttm) REVERT: b 29 MET cc_start: 0.2216 (ttt) cc_final: 0.1084 (tmm) REVERT: b 396 MET cc_start: 0.8886 (mtp) cc_final: 0.8044 (mtp) REVERT: a 1 MET cc_start: 0.7060 (ptp) cc_final: 0.6492 (ptp) REVERT: a 219 MET cc_start: 0.9107 (mmp) cc_final: 0.8791 (mmm) REVERT: a 327 MET cc_start: 0.8648 (mmp) cc_final: 0.8424 (mmm) REVERT: a 390 MET cc_start: 0.7151 (pmm) cc_final: 0.6815 (pmm) REVERT: d 29 MET cc_start: 0.2387 (ptm) cc_final: 0.2064 (tmm) REVERT: d 147 MET cc_start: 0.8650 (tpt) cc_final: 0.7822 (tpt) REVERT: d 327 MET cc_start: 0.8626 (tpt) cc_final: 0.8407 (tpp) REVERT: d 390 MET cc_start: 0.7103 (ptp) cc_final: 0.6274 (ptt) REVERT: d 396 MET cc_start: 0.9480 (mtt) cc_final: 0.9156 (mtp) REVERT: d 416 MET cc_start: 0.6051 (ptt) cc_final: 0.5452 (ptt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3014 time to fit residues: 51.8736 Evaluate side-chains 99 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 5 optimal weight: 6.9990 chunk 233 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 230 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.032377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.025939 restraints weight = 377205.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.026217 restraints weight = 338110.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.026398 restraints weight = 308102.313| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.8056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20379 Z= 0.092 Angle : 0.583 9.217 27469 Z= 0.274 Chirality : 0.042 0.185 3130 Planarity : 0.003 0.042 3524 Dihedral : 9.609 162.720 2901 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2490 helix: 1.45 (0.16), residues: 1158 sheet: -0.23 (0.26), residues: 402 loop : 0.75 (0.23), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 381 HIS 0.004 0.001 HIS f 344 PHE 0.012 0.001 PHE d 355 TYR 0.016 0.001 TYR d 332 ARG 0.006 0.000 ARG b 252 Details of bonding type rmsd hydrogen bonds : bond 0.02332 ( 944) hydrogen bonds : angle 3.91611 ( 2742) covalent geometry : bond 0.00197 (20349) covalent geometry : angle 0.58286 (27469) Misc. bond : bond 0.00252 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5865.17 seconds wall clock time: 103 minutes 5.46 seconds (6185.46 seconds total)