Starting phenix.real_space_refine on Tue Jun 17 20:54:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5l_27914/06_2025/8e5l_27914_neut.cif" } resolution = 4.2 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 21 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12533 2.51 5 N 3540 2.21 5 O 3832 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20058 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.89, per 1000 atoms: 0.69 Number of scatterers: 20058 At special positions: 0 Unit cell: (145.32, 126.636, 137.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 21 15.00 Mg 6 11.99 F 18 9.00 O 3832 8.00 N 3540 7.00 C 12533 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 2.8 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: 2.45 Creating SS restraints... Processing helix chain 'e' and resid 2 through 9 Processing helix chain 'e' and resid 10 through 22 Processing helix chain 'e' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 132 through 136 Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 235 through 255 Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 338 removed outlier: 3.554A pdb=" N GLU e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 371 Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 391 through 404 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS e 417 " --> pdb=" O PHE e 413 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 Processing helix chain 'f' and resid 10 through 22 Processing helix chain 'f' and resid 30 through 45 removed outlier: 3.705A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 90 Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 132 through 136 Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.268A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 221 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 335 removed outlier: 3.717A pdb=" N GLU f 329 " --> pdb=" O SER f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 371 Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 391 through 404 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.718A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS f 417 " --> pdb=" O PHE f 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 Processing helix chain 'c' and resid 10 through 22 Processing helix chain 'c' and resid 30 through 45 removed outlier: 3.701A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 90 Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.270A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 221 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU c 333 " --> pdb=" O GLU c 329 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 371 Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 391 through 404 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS c 417 " --> pdb=" O PHE c 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 Processing helix chain 'b' and resid 10 through 22 Processing helix chain 'b' and resid 30 through 45 removed outlier: 3.704A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 90 Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 132 through 136 Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 221 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.595A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 335 removed outlier: 3.643A pdb=" N GLU b 333 " --> pdb=" O GLU b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.554A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 391 through 404 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.722A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS b 417 " --> pdb=" O PHE b 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 10 through 22 Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.702A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 90 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 132 through 136 Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 221 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 337 removed outlier: 4.203A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 371 Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 391 through 404 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.720A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS a 417 " --> pdb=" O PHE a 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 Processing helix chain 'd' and resid 10 through 22 Processing helix chain 'd' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 90 Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.267A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 221 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.593A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 333 Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 371 Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 391 through 404 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR e 96 " --> pdb=" O VAL e 119 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL e 119 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER e 98 " --> pdb=" O ASN e 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS e 115 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG e 102 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.802A pdb=" N ASN e 306 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.476A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA e 317 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU e 342 " --> pdb=" O GLY e 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY e 364 " --> pdb=" O GLU e 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR f 96 " --> pdb=" O VAL f 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL f 119 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER f 98 " --> pdb=" O ASN f 117 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS f 115 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG f 102 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU f 113 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.805A pdb=" N ASN f 306 " --> pdb=" O LEU f 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.480A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA f 317 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU f 342 " --> pdb=" O GLY f 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY f 364 " --> pdb=" O GLU f 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR c 96 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL c 119 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER c 98 " --> pdb=" O ASN c 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS c 115 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG c 102 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN c 306 " --> pdb=" O LEU c 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.479A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 173 through 178 removed outlier: 3.631A pdb=" N ALA c 317 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU c 342 " --> pdb=" O GLY c 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY c 364 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 63 through 66 removed outlier: 3.854A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR b 96 " --> pdb=" O VAL b 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 119 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 98 " --> pdb=" O ASN b 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS b 115 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG b 102 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU b 113 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN b 306 " --> pdb=" O LEU b 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA b 317 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 341 through 342 removed outlier: 3.903A pdb=" N GLU b 342 " --> pdb=" O GLY b 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY b 364 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'a' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR a 96 " --> pdb=" O VAL a 119 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL a 119 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER a 98 " --> pdb=" O ASN a 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS a 115 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG a 102 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN a 306 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 173 through 178 removed outlier: 3.633A pdb=" N ALA a 317 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU a 342 " --> pdb=" O GLY a 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY a 364 " --> pdb=" O GLU a 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 63 through 66 removed outlier: 3.852A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR d 96 " --> pdb=" O VAL d 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL d 119 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER d 98 " --> pdb=" O ASN d 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS d 115 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG d 102 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU d 113 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.806A pdb=" N ASN d 306 " --> pdb=" O LEU d 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.477A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA d 317 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 341 through 342 removed outlier: 3.904A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 364 " --> pdb=" O GLU d 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 944 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.75 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4755 1.33 - 1.45: 3619 1.45 - 1.57: 11764 1.57 - 1.69: 35 1.69 - 1.81: 198 Bond restraints: 20371 Sorted by residual: bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF f1002 " pdb="BE BEF f1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 27286 2.88 - 5.77: 167 5.77 - 8.65: 38 8.65 - 11.53: 6 11.53 - 14.41: 6 Bond angle restraints: 27503 Sorted by residual: angle pdb=" N ASP f 322 " pdb=" CA ASP f 322 " pdb=" C ASP f 322 " ideal model delta sigma weight residual 112.58 105.31 7.27 1.22e+00 6.72e-01 3.55e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.73 6.60 1.21e+00 6.83e-01 2.97e+01 angle pdb=" N GLU c 334 " pdb=" CA GLU c 334 " pdb=" C GLU c 334 " ideal model delta sigma weight residual 111.33 105.04 6.29 1.21e+00 6.83e-01 2.70e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 12396 29.81 - 59.62: 154 59.62 - 89.43: 45 89.43 - 119.24: 2 119.24 - 149.05: 10 Dihedral angle restraints: 12607 sinusoidal: 5413 harmonic: 7194 Sorted by residual: dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.05 -149.05 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP e1000 " pdb=" O3A ADP e1000 " pdb=" PB ADP e1000 " pdb=" PA ADP e1000 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.98 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PA ADP d1000 " pdb=" PB ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 84.41 -144.41 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2600 0.052 - 0.103: 412 0.103 - 0.155: 112 0.155 - 0.206: 10 0.206 - 0.258: 1 Chirality restraints: 3135 Sorted by residual: chirality pdb=" C3' A 7 1 " pdb=" C4' A 7 1 " pdb=" O3' A 7 1 " pdb=" C2' A 7 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL d 330 " pdb=" N VAL d 330 " pdb=" C VAL d 330 " pdb=" CB VAL d 330 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" C3' U 7 2 " pdb=" C4' U 7 2 " pdb=" O3' U 7 2 " pdb=" C2' U 7 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3132 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.48e-02 4.19e+01 pdb=" C ILE b 331 " -0.112 2.00e-02 2.50e+03 pdb=" O ILE b 331 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR b 332 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 331 " -0.028 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C ILE e 331 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE e 331 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR e 332 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 331 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE c 331 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE c 331 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR c 332 " 0.028 2.00e-02 2.50e+03 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 55 2.02 - 2.74: 1642 2.74 - 3.46: 29057 3.46 - 4.18: 46275 4.18 - 4.90: 83659 Nonbonded interactions: 160688 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 3.040 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 nonbonded pdb=" NH1 ARG e 272 " pdb=" OE2 GLU f 334 " model vdw 1.416 3.120 nonbonded pdb=" NZ LYS e 385 " pdb=" O LYS d 352 " model vdw 1.495 3.120 ... (remaining 160683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 48.980 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.748 20401 Z= 1.843 Angle : 0.641 14.413 27503 Z= 0.351 Chirality : 0.042 0.258 3135 Planarity : 0.004 0.065 3525 Dihedral : 11.889 149.051 7951 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 4.11 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.001 0.000 HIS e 295 PHE 0.007 0.001 PHE a 36 TYR 0.016 0.001 TYR d 332 ARG 0.003 0.000 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.19912 ( 944) hydrogen bonds : angle 6.53638 ( 2742) covalent geometry : bond 0.00342 (20371) covalent geometry : angle 0.64137 (27503) Misc. bond : bond 0.47746 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.1134 (mmm) cc_final: -0.0696 (ttt) REVERT: c 29 MET cc_start: -0.1502 (mtp) cc_final: -0.2170 (ttt) REVERT: b 29 MET cc_start: -0.1529 (mtp) cc_final: -0.2116 (ttt) REVERT: d 21 MET cc_start: -0.0973 (mmm) cc_final: -0.4034 (ttt) outliers start: 35 outliers final: 8 residues processed: 269 average time/residue: 0.3634 time to fit residues: 144.1013 Evaluate side-chains 147 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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: 3.9990 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 193 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 135 ASN e 241 GLN e 256 HIS f 126 ASN f 135 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 ASN c 241 GLN c 295 HIS c 340 ASN b 25 ASN b 135 ASN b 220 GLN b 241 GLN b 256 HIS a 256 HIS d 135 ASN d 241 GLN d 256 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.034920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.027883 restraints weight = 331080.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.028473 restraints weight = 256996.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.028903 restraints weight = 211841.363| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20401 Z= 0.229 Angle : 0.791 9.441 27503 Z= 0.389 Chirality : 0.045 0.174 3135 Planarity : 0.005 0.054 3525 Dihedral : 10.926 162.167 2917 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.23 % Allowed : 3.03 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.17), residues: 2490 helix: 0.24 (0.15), residues: 1158 sheet: -0.84 (0.25), residues: 408 loop : 0.12 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 381 HIS 0.011 0.002 HIS c 388 PHE 0.019 0.002 PHE b 335 TYR 0.021 0.002 TYR d 332 ARG 0.010 0.001 ARG c 66 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 944) hydrogen bonds : angle 4.77965 ( 2742) covalent geometry : bond 0.00475 (20371) covalent geometry : angle 0.79065 (27503) Misc. bond : bond 0.00335 ( 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 151 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.1043 (ttt) cc_final: -0.1282 (ttt) REVERT: e 207 LEU cc_start: 0.9321 (mp) cc_final: 0.8944 (mp) REVERT: e 341 MET cc_start: 0.1175 (mtp) cc_final: 0.0819 (mtm) REVERT: f 21 MET cc_start: -0.2009 (mmm) cc_final: -0.2667 (mtm) REVERT: f 36 PHE cc_start: 0.9280 (t80) cc_final: 0.9077 (t80) REVERT: f 219 MET cc_start: 0.9440 (mmp) cc_final: 0.9034 (mmm) REVERT: f 396 MET cc_start: 0.9226 (mmp) cc_final: 0.8990 (mmm) REVERT: f 413 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: c 147 MET cc_start: 0.6482 (tpt) cc_final: 0.5581 (mpp) REVERT: c 416 MET cc_start: 0.4677 (ptm) cc_final: 0.4435 (ptt) REVERT: b 29 MET cc_start: 0.2580 (mtp) cc_final: 0.1765 (ttt) REVERT: b 111 PHE cc_start: 0.8977 (m-80) cc_final: 0.8470 (m-80) REVERT: a 132 LEU cc_start: 0.9696 (mt) cc_final: 0.9491 (mt) REVERT: a 147 MET cc_start: 0.8781 (tpp) cc_final: 0.8238 (tpp) REVERT: d 21 MET cc_start: -0.4162 (mmm) cc_final: -0.4493 (mtt) REVERT: d 29 MET cc_start: 0.8791 (ttp) cc_final: 0.8454 (ptm) REVERT: d 147 MET cc_start: 0.8495 (mmp) cc_final: 0.7533 (tpt) REVERT: d 380 MET cc_start: 0.9058 (mmp) cc_final: 0.8858 (mmm) outliers start: 5 outliers final: 1 residues processed: 151 average time/residue: 0.3210 time to fit residues: 75.8352 Evaluate side-chains 121 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 236 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 chunk 155 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN f 172 GLN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN c 388 HIS ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 HIS ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.032573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.025843 restraints weight = 338587.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.026449 restraints weight = 254845.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.026886 restraints weight = 206133.468| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20401 Z= 0.170 Angle : 0.665 7.547 27503 Z= 0.327 Chirality : 0.043 0.153 3135 Planarity : 0.004 0.038 3525 Dihedral : 10.270 170.508 2917 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 0.29 (0.17), residues: 2490 helix: 0.58 (0.15), residues: 1170 sheet: -0.60 (0.26), residues: 390 loop : 0.31 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.007 0.001 HIS c 388 PHE 0.042 0.002 PHE f 36 TYR 0.017 0.002 TYR f 332 ARG 0.007 0.001 ARG f 221 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 944) hydrogen bonds : angle 4.43510 ( 2742) covalent geometry : bond 0.00347 (20371) covalent geometry : angle 0.66548 (27503) Misc. bond : bond 0.00300 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 327 MET cc_start: 0.9657 (tmm) cc_final: 0.9416 (tmm) REVERT: f 1 MET cc_start: 0.5180 (pmm) cc_final: 0.4969 (pmm) REVERT: f 21 MET cc_start: -0.0685 (mmm) cc_final: -0.1995 (mtm) REVERT: f 29 MET cc_start: 0.2773 (ttm) cc_final: 0.2454 (ptm) REVERT: f 219 MET cc_start: 0.9070 (mmp) cc_final: 0.8696 (mmm) REVERT: f 396 MET cc_start: 0.9087 (mmp) cc_final: 0.8842 (mtp) REVERT: c 1 MET cc_start: 0.9334 (mpp) cc_final: 0.9113 (mpp) REVERT: c 147 MET cc_start: 0.6378 (tpt) cc_final: 0.5493 (mpp) REVERT: b 72 TYR cc_start: 0.9163 (m-10) cc_final: 0.8953 (m-10) REVERT: b 111 PHE cc_start: 0.8976 (m-80) cc_final: 0.8517 (m-80) REVERT: b 341 MET cc_start: 0.2668 (mmm) cc_final: 0.1852 (mmp) REVERT: a 29 MET cc_start: 0.3787 (ttm) cc_final: 0.3547 (ttm) REVERT: d 21 MET cc_start: -0.3383 (mmm) cc_final: -0.3643 (mtm) REVERT: d 147 MET cc_start: 0.8543 (mmp) cc_final: 0.7843 (tpt) REVERT: d 327 MET cc_start: 0.7658 (ttt) cc_final: 0.7383 (tmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3218 time to fit residues: 66.9262 Evaluate side-chains 115 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 69 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 0.0040 chunk 187 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 ASN e 172 GLN e 220 GLN e 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.030764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.024305 restraints weight = 348119.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.024891 restraints weight = 260515.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.025301 restraints weight = 209714.831| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20401 Z= 0.152 Angle : 0.634 7.053 27503 Z= 0.308 Chirality : 0.042 0.144 3135 Planarity : 0.004 0.036 3525 Dihedral : 10.193 163.220 2917 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.17), residues: 2490 helix: 0.68 (0.14), residues: 1188 sheet: -0.57 (0.26), residues: 390 loop : 0.50 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.006 0.001 HIS a 344 PHE 0.011 0.001 PHE d 62 TYR 0.022 0.002 TYR f 332 ARG 0.005 0.001 ARG f 66 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 944) hydrogen bonds : angle 4.39485 ( 2742) covalent geometry : bond 0.00312 (20371) covalent geometry : angle 0.63400 (27503) Misc. bond : bond 0.00265 ( 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 129 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.0462 (ttt) cc_final: -0.0804 (ttt) REVERT: e 29 MET cc_start: 0.6263 (ttm) cc_final: 0.5809 (ttp) REVERT: e 205 MET cc_start: 0.8488 (tpt) cc_final: 0.8236 (tpt) REVERT: f 207 LEU cc_start: 0.9291 (pt) cc_final: 0.8911 (tp) REVERT: f 219 MET cc_start: 0.9211 (mmp) cc_final: 0.8821 (mmm) REVERT: f 341 MET cc_start: 0.4812 (tmm) cc_final: 0.4357 (tmm) REVERT: f 396 MET cc_start: 0.9198 (mmp) cc_final: 0.8864 (mtp) REVERT: c 1 MET cc_start: 0.9454 (mpp) cc_final: 0.9163 (mpp) REVERT: c 147 MET cc_start: 0.6473 (tpt) cc_final: 0.5658 (mpp) REVERT: c 390 MET cc_start: 0.8703 (ptt) cc_final: 0.8269 (ptt) REVERT: b 8 ASN cc_start: 0.9392 (m-40) cc_final: 0.9027 (p0) REVERT: b 29 MET cc_start: 0.4673 (mtp) cc_final: 0.4273 (ttp) REVERT: b 72 TYR cc_start: 0.9272 (m-80) cc_final: 0.8992 (m-10) REVERT: b 111 PHE cc_start: 0.9104 (m-80) cc_final: 0.8585 (m-80) REVERT: b 147 MET cc_start: 0.8440 (mpp) cc_final: 0.7158 (tpt) REVERT: b 207 LEU cc_start: 0.9458 (mp) cc_final: 0.9212 (tt) REVERT: b 245 MET cc_start: 0.8738 (ptp) cc_final: 0.8258 (ptp) REVERT: b 341 MET cc_start: 0.2891 (mmm) cc_final: 0.1882 (mmt) REVERT: a 29 MET cc_start: 0.3284 (ttp) cc_final: 0.2904 (ptm) REVERT: a 245 MET cc_start: 0.9287 (ptp) cc_final: 0.8459 (ptp) REVERT: d 8 ASN cc_start: 0.9376 (m-40) cc_final: 0.9131 (p0) REVERT: d 29 MET cc_start: 0.8802 (ttp) cc_final: 0.8532 (ptm) REVERT: d 147 MET cc_start: 0.8529 (mmp) cc_final: 0.7805 (tpt) REVERT: d 186 MET cc_start: 0.9379 (tmm) cc_final: 0.9060 (tmm) REVERT: d 327 MET cc_start: 0.7180 (ttt) cc_final: 0.6865 (tmm) REVERT: d 341 MET cc_start: 0.0270 (mmm) cc_final: -0.0351 (tpt) REVERT: d 415 MET cc_start: 0.7978 (mpp) cc_final: 0.7723 (ptp) REVERT: d 416 MET cc_start: 0.1358 (ptt) cc_final: 0.1155 (ptt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3251 time to fit residues: 66.7694 Evaluate side-chains 112 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 0.2980 chunk 218 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** f 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** ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS b 239 HIS a 32 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.031162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.024692 restraints weight = 341738.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.025286 restraints weight = 252887.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.025726 restraints weight = 202966.119| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20401 Z= 0.104 Angle : 0.569 6.583 27503 Z= 0.272 Chirality : 0.041 0.134 3135 Planarity : 0.003 0.037 3525 Dihedral : 9.878 164.397 2917 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 0.82 (0.17), residues: 2490 helix: 1.08 (0.15), residues: 1182 sheet: -0.52 (0.26), residues: 390 loop : 0.58 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 381 HIS 0.007 0.001 HIS b 344 PHE 0.016 0.001 PHE f 36 TYR 0.012 0.001 TYR f 332 ARG 0.003 0.000 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.02500 ( 944) hydrogen bonds : angle 4.17136 ( 2742) covalent geometry : bond 0.00221 (20371) covalent geometry : angle 0.56860 (27503) Misc. bond : bond 0.00247 ( 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 123 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 MET cc_start: 0.6258 (ttm) cc_final: 0.5726 (ttp) REVERT: f 29 MET cc_start: 0.2615 (ttm) cc_final: 0.2230 (ptm) REVERT: f 207 LEU cc_start: 0.9319 (pt) cc_final: 0.8890 (tp) REVERT: f 219 MET cc_start: 0.9084 (mmp) cc_final: 0.8714 (mmm) REVERT: f 396 MET cc_start: 0.9184 (mmp) cc_final: 0.8932 (mtp) REVERT: c 147 MET cc_start: 0.6631 (tpt) cc_final: 0.5785 (mpp) REVERT: c 390 MET cc_start: 0.8703 (ptt) cc_final: 0.8185 (ptt) REVERT: b 8 ASN cc_start: 0.9371 (m-40) cc_final: 0.9013 (p0) REVERT: b 29 MET cc_start: 0.4860 (mtp) cc_final: 0.4407 (ttp) REVERT: b 72 TYR cc_start: 0.9207 (m-80) cc_final: 0.8881 (m-10) REVERT: b 111 PHE cc_start: 0.9062 (m-80) cc_final: 0.8505 (m-80) REVERT: b 147 MET cc_start: 0.8545 (mpp) cc_final: 0.7298 (tpt) REVERT: b 245 MET cc_start: 0.8697 (ptp) cc_final: 0.8218 (ptp) REVERT: b 327 MET cc_start: 0.7312 (tmm) cc_final: 0.7085 (tmm) REVERT: a 1 MET cc_start: 0.7606 (pmm) cc_final: 0.7291 (pmm) REVERT: a 396 MET cc_start: 0.8993 (mtt) cc_final: 0.8512 (mtp) REVERT: d 8 ASN cc_start: 0.9415 (m-40) cc_final: 0.9189 (p0) REVERT: d 21 MET cc_start: -0.2458 (mtp) cc_final: -0.2674 (ttp) REVERT: d 147 MET cc_start: 0.8432 (mmp) cc_final: 0.7714 (tpt) REVERT: d 327 MET cc_start: 0.7407 (ttt) cc_final: 0.7079 (tmm) REVERT: d 341 MET cc_start: -0.0032 (mmm) cc_final: -0.0481 (tpt) REVERT: d 390 MET cc_start: 0.8619 (pmm) cc_final: 0.8351 (pmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3000 time to fit residues: 59.5635 Evaluate side-chains 110 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 98 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 120 optimal weight: 0.0870 overall best weight: 4.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 ASN a 142 ASN d 190 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.028029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.021960 restraints weight = 364922.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.022513 restraints weight = 272086.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.022912 restraints weight = 218453.174| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.8761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20401 Z= 0.202 Angle : 0.718 8.146 27503 Z= 0.352 Chirality : 0.043 0.165 3135 Planarity : 0.004 0.043 3525 Dihedral : 10.240 166.652 2917 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.17), residues: 2490 helix: 0.58 (0.14), residues: 1182 sheet: -0.69 (0.26), residues: 384 loop : 0.51 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 381 HIS 0.009 0.002 HIS c 344 PHE 0.018 0.002 PHE d 62 TYR 0.031 0.002 TYR c 332 ARG 0.008 0.001 ARG e 221 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 944) hydrogen bonds : angle 4.67126 ( 2742) covalent geometry : bond 0.00409 (20371) covalent geometry : angle 0.71838 (27503) Misc. bond : bond 0.00219 ( 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 120 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.493 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: -0.0659 (ttt) cc_final: -0.1164 (ttt) REVERT: e 29 MET cc_start: 0.6922 (ttm) cc_final: 0.6566 (ttp) REVERT: e 36 PHE cc_start: 0.9613 (t80) cc_final: 0.9219 (t80) REVERT: f 1 MET cc_start: 0.5950 (pmm) cc_final: 0.5704 (pmm) REVERT: f 207 LEU cc_start: 0.9326 (pt) cc_final: 0.9042 (tp) REVERT: f 219 MET cc_start: 0.9184 (mmp) cc_final: 0.8948 (mmm) REVERT: f 341 MET cc_start: 0.5868 (tmm) cc_final: 0.5565 (tmm) REVERT: f 396 MET cc_start: 0.9201 (mmp) cc_final: 0.8894 (mmm) REVERT: c 147 MET cc_start: 0.6458 (tpt) cc_final: 0.5859 (mpp) REVERT: c 390 MET cc_start: 0.8913 (ptt) cc_final: 0.8397 (ptp) REVERT: b 8 ASN cc_start: 0.9375 (m-40) cc_final: 0.8997 (p0) REVERT: b 29 MET cc_start: 0.5685 (mtp) cc_final: 0.5369 (ttp) REVERT: b 72 TYR cc_start: 0.9332 (m-80) cc_final: 0.9043 (m-10) REVERT: b 147 MET cc_start: 0.8912 (mpp) cc_final: 0.7340 (tpt) REVERT: b 245 MET cc_start: 0.8631 (ptp) cc_final: 0.8253 (ptp) REVERT: b 327 MET cc_start: 0.7976 (tmm) cc_final: 0.7759 (tmm) REVERT: a 1 MET cc_start: 0.7433 (pmm) cc_final: 0.7075 (pmm) REVERT: a 29 MET cc_start: 0.3986 (ptm) cc_final: 0.3595 (ptm) REVERT: a 72 TYR cc_start: 0.9162 (m-10) cc_final: 0.8844 (m-10) REVERT: a 147 MET cc_start: 0.7032 (tpt) cc_final: 0.6250 (mpp) REVERT: a 245 MET cc_start: 0.9265 (ptp) cc_final: 0.8811 (ptp) REVERT: a 390 MET cc_start: 0.9022 (ptt) cc_final: 0.8764 (ptt) REVERT: a 396 MET cc_start: 0.9023 (mtt) cc_final: 0.8553 (mmm) REVERT: d 8 ASN cc_start: 0.9421 (m-40) cc_final: 0.9187 (p0) REVERT: d 147 MET cc_start: 0.8602 (mmp) cc_final: 0.7808 (tpt) REVERT: d 327 MET cc_start: 0.7354 (ttt) cc_final: 0.6946 (tmm) REVERT: d 390 MET cc_start: 0.8836 (pmm) cc_final: 0.8571 (pmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3154 time to fit residues: 61.3075 Evaluate side-chains 109 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 169 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 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 241 GLN f 388 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 220 GLN a 20 ASN a 32 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.027671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.021710 restraints weight = 363898.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.022264 restraints weight = 268520.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.022663 restraints weight = 214074.979| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.9418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20401 Z= 0.160 Angle : 0.655 8.059 27503 Z= 0.316 Chirality : 0.042 0.221 3135 Planarity : 0.004 0.077 3525 Dihedral : 10.106 160.896 2917 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.52 (0.17), residues: 2490 helix: 0.77 (0.15), residues: 1152 sheet: -0.71 (0.26), residues: 384 loop : 0.55 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 381 HIS 0.006 0.001 HIS a 344 PHE 0.017 0.002 PHE e 36 TYR 0.016 0.001 TYR c 332 ARG 0.011 0.001 ARG c 366 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 944) hydrogen bonds : angle 4.51388 ( 2742) covalent geometry : bond 0.00330 (20371) covalent geometry : angle 0.65472 (27503) Misc. bond : bond 0.00378 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.299 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: 0.0079 (ttt) cc_final: -0.0307 (ttt) REVERT: e 29 MET cc_start: 0.6937 (ttm) cc_final: 0.6608 (ttp) REVERT: e 147 MET cc_start: 0.7712 (mpp) cc_final: 0.7349 (mpp) REVERT: e 207 LEU cc_start: 0.9456 (pt) cc_final: 0.9251 (pt) REVERT: f 1 MET cc_start: 0.6325 (pmm) cc_final: 0.6029 (pmm) REVERT: f 207 LEU cc_start: 0.9343 (pt) cc_final: 0.9112 (tp) REVERT: f 219 MET cc_start: 0.9127 (mmp) cc_final: 0.8863 (mmm) REVERT: f 341 MET cc_start: 0.6379 (tmm) cc_final: 0.6069 (tmm) REVERT: f 390 MET cc_start: 0.8235 (pmm) cc_final: 0.7829 (pmm) REVERT: f 396 MET cc_start: 0.9216 (mmp) cc_final: 0.8828 (mmm) REVERT: c 147 MET cc_start: 0.6546 (tpt) cc_final: 0.5913 (mpp) REVERT: c 390 MET cc_start: 0.9014 (ptt) cc_final: 0.8507 (ptt) REVERT: b 29 MET cc_start: 0.6089 (mtp) cc_final: 0.5374 (mtp) REVERT: b 245 MET cc_start: 0.8602 (ptp) cc_final: 0.8345 (ptp) REVERT: b 341 MET cc_start: 0.4678 (mmm) cc_final: 0.4399 (mmm) REVERT: b 396 MET cc_start: 0.8978 (mmm) cc_final: 0.8145 (mmm) REVERT: a 1 MET cc_start: 0.7230 (pmm) cc_final: 0.6043 (ptp) REVERT: a 8 ASN cc_start: 0.9680 (m-40) cc_final: 0.9458 (p0) REVERT: a 29 MET cc_start: 0.3887 (ptm) cc_final: 0.3564 (ptm) REVERT: a 147 MET cc_start: 0.7292 (tpt) cc_final: 0.6707 (mpp) REVERT: a 390 MET cc_start: 0.9076 (ptt) cc_final: 0.8660 (ptt) REVERT: a 396 MET cc_start: 0.9075 (mtt) cc_final: 0.8662 (mtp) REVERT: d 21 MET cc_start: -0.1608 (mtp) cc_final: -0.1917 (ttp) REVERT: d 147 MET cc_start: 0.8474 (mmp) cc_final: 0.7732 (tpt) REVERT: d 327 MET cc_start: 0.7571 (ttt) cc_final: 0.7186 (tmm) REVERT: d 341 MET cc_start: 0.1546 (mmp) cc_final: 0.0909 (tpp) REVERT: d 390 MET cc_start: 0.8771 (pmm) cc_final: 0.8491 (pmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3181 time to fit residues: 61.5516 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 : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 33 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 246 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN e 344 HIS f 32 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.027267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.021347 restraints weight = 365813.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.021896 restraints weight = 270121.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.022297 restraints weight = 215405.335| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.9932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20401 Z= 0.141 Angle : 0.627 7.708 27503 Z= 0.303 Chirality : 0.042 0.199 3135 Planarity : 0.004 0.043 3525 Dihedral : 9.930 161.690 2917 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.17), residues: 2490 helix: 0.90 (0.15), residues: 1182 sheet: -0.69 (0.26), residues: 390 loop : 0.47 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 381 HIS 0.010 0.001 HIS e 344 PHE 0.013 0.001 PHE e 50 TYR 0.015 0.002 TYR d 332 ARG 0.004 0.001 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 944) hydrogen bonds : angle 4.49511 ( 2742) covalent geometry : bond 0.00292 (20371) covalent geometry : angle 0.62676 (27503) Misc. bond : bond 0.00339 ( 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 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 2.577 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: 0.0155 (ttt) cc_final: -0.0121 (ttt) REVERT: e 147 MET cc_start: 0.7721 (mpp) cc_final: 0.5405 (tpp) REVERT: e 207 LEU cc_start: 0.9495 (pt) cc_final: 0.9209 (pt) REVERT: e 396 MET cc_start: 0.9034 (ttt) cc_final: 0.8729 (ptt) REVERT: f 29 MET cc_start: 0.2400 (ptm) cc_final: 0.1806 (tmm) REVERT: f 207 LEU cc_start: 0.9366 (pt) cc_final: 0.9060 (tp) REVERT: f 341 MET cc_start: 0.6681 (tmm) cc_final: 0.6454 (tmm) REVERT: f 390 MET cc_start: 0.8239 (pmm) cc_final: 0.7778 (pmm) REVERT: f 396 MET cc_start: 0.9210 (mmp) cc_final: 0.8780 (mmm) REVERT: c 147 MET cc_start: 0.6411 (tpt) cc_final: 0.5751 (mpp) REVERT: c 390 MET cc_start: 0.9101 (ptt) cc_final: 0.8533 (ptt) REVERT: b 29 MET cc_start: 0.6213 (mtp) cc_final: 0.5539 (mtp) REVERT: b 111 PHE cc_start: 0.9184 (m-80) cc_final: 0.8640 (m-80) REVERT: b 245 MET cc_start: 0.8515 (ptp) cc_final: 0.8276 (ptp) REVERT: b 327 MET cc_start: 0.7980 (tmm) cc_final: 0.7647 (tmm) REVERT: b 341 MET cc_start: 0.4647 (mmm) cc_final: 0.4415 (mmm) REVERT: b 396 MET cc_start: 0.9009 (mmm) cc_final: 0.8279 (mmp) REVERT: a 1 MET cc_start: 0.7014 (pmm) cc_final: 0.6061 (ptp) REVERT: a 29 MET cc_start: 0.4105 (ptm) cc_final: 0.3805 (ptm) REVERT: a 147 MET cc_start: 0.7503 (tpt) cc_final: 0.6955 (mpp) REVERT: a 390 MET cc_start: 0.9107 (ptt) cc_final: 0.8669 (ptt) REVERT: a 396 MET cc_start: 0.9133 (mtt) cc_final: 0.8747 (mtp) REVERT: d 21 MET cc_start: -0.1175 (mtp) cc_final: -0.1544 (ttp) REVERT: d 29 MET cc_start: 0.8401 (pmm) cc_final: 0.8103 (pmm) REVERT: d 147 MET cc_start: 0.7963 (mmp) cc_final: 0.7184 (tpt) REVERT: d 327 MET cc_start: 0.7620 (ttt) cc_final: 0.7198 (tmm) REVERT: d 341 MET cc_start: 0.1932 (mmp) cc_final: 0.1114 (tpp) REVERT: d 390 MET cc_start: 0.8724 (pmm) cc_final: 0.8471 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3274 time to fit residues: 61.7807 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 : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 156 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 20 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.027515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.021566 restraints weight = 361953.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.022111 restraints weight = 266198.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.022514 restraints weight = 212496.930| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 1.0147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20401 Z= 0.115 Angle : 0.601 8.563 27503 Z= 0.288 Chirality : 0.042 0.166 3135 Planarity : 0.004 0.045 3525 Dihedral : 9.812 161.430 2917 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 0.78 (0.17), residues: 2490 helix: 1.10 (0.15), residues: 1176 sheet: -0.61 (0.26), residues: 390 loop : 0.51 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 381 HIS 0.005 0.001 HIS c 344 PHE 0.027 0.001 PHE b 335 TYR 0.014 0.001 TYR d 332 ARG 0.004 0.000 ARG d 221 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 944) hydrogen bonds : angle 4.37972 ( 2742) covalent geometry : bond 0.00244 (20371) covalent geometry : angle 0.60146 (27503) Misc. bond : bond 0.00312 ( 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 119 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 147 MET cc_start: 0.7149 (mpp) cc_final: 0.5034 (tpp) REVERT: f 1 MET cc_start: 0.6200 (pmm) cc_final: 0.5992 (pmm) REVERT: f 390 MET cc_start: 0.7847 (pmm) cc_final: 0.7579 (pmm) REVERT: c 147 MET cc_start: 0.5829 (tpt) cc_final: 0.5539 (mpp) REVERT: c 327 MET cc_start: 0.6928 (ttt) cc_final: 0.6101 (tmm) REVERT: c 390 MET cc_start: 0.8872 (ptt) cc_final: 0.8188 (ptt) REVERT: b 29 MET cc_start: 0.5886 (mtp) cc_final: 0.5327 (mtp) REVERT: b 72 TYR cc_start: 0.8856 (m-80) cc_final: 0.8469 (m-80) REVERT: b 111 PHE cc_start: 0.8563 (m-80) cc_final: 0.8179 (m-80) REVERT: b 245 MET cc_start: 0.8341 (ptp) cc_final: 0.8034 (ptp) REVERT: b 327 MET cc_start: 0.7784 (tmm) cc_final: 0.7546 (tmm) REVERT: b 341 MET cc_start: 0.4446 (mmm) cc_final: 0.3766 (mmm) REVERT: b 396 MET cc_start: 0.8525 (mmm) cc_final: 0.8049 (mmp) REVERT: a 1 MET cc_start: 0.6868 (pmm) cc_final: 0.5763 (ptp) REVERT: a 29 MET cc_start: 0.3127 (ptm) cc_final: 0.2869 (ptm) REVERT: a 245 MET cc_start: 0.8962 (ptp) cc_final: 0.8636 (ptp) REVERT: a 396 MET cc_start: 0.8574 (mtt) cc_final: 0.8366 (mtp) REVERT: d 21 MET cc_start: -0.1648 (mtp) cc_final: -0.1868 (ttp) REVERT: d 29 MET cc_start: 0.7758 (pmm) cc_final: 0.6084 (pmm) REVERT: d 147 MET cc_start: 0.7365 (mmp) cc_final: 0.6686 (tpt) REVERT: d 327 MET cc_start: 0.7595 (ttt) cc_final: 0.7161 (tmm) REVERT: d 341 MET cc_start: 0.1495 (mmp) cc_final: 0.0915 (tpp) REVERT: d 390 MET cc_start: 0.8541 (pmm) cc_final: 0.8268 (pmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3320 time to fit residues: 63.0025 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 : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.027738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.021779 restraints weight = 360062.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.022336 restraints weight = 264031.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.022743 restraints weight = 210166.397| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.0299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20401 Z= 0.105 Angle : 0.606 9.030 27503 Z= 0.287 Chirality : 0.042 0.197 3135 Planarity : 0.004 0.048 3525 Dihedral : 9.741 160.843 2917 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2490 helix: 1.21 (0.15), residues: 1176 sheet: -0.82 (0.25), residues: 432 loop : 0.64 (0.24), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 381 HIS 0.005 0.001 HIS c 344 PHE 0.026 0.001 PHE e 36 TYR 0.013 0.001 TYR f 332 ARG 0.004 0.000 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.02578 ( 944) hydrogen bonds : angle 4.33222 ( 2742) covalent geometry : bond 0.00224 (20371) covalent geometry : angle 0.60550 (27503) Misc. bond : bond 0.00331 ( 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 117 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 2.308 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 147 MET cc_start: 0.7254 (mpp) cc_final: 0.5140 (tpp) REVERT: f 1 MET cc_start: 0.6313 (pmm) cc_final: 0.6106 (pmm) REVERT: f 29 MET cc_start: 0.2458 (tmm) cc_final: 0.2063 (tmm) REVERT: c 147 MET cc_start: 0.5690 (tpt) cc_final: 0.5437 (mpp) REVERT: c 327 MET cc_start: 0.6994 (ttt) cc_final: 0.6232 (tmm) REVERT: c 380 MET cc_start: 0.9218 (mmp) cc_final: 0.8853 (tmm) REVERT: b 29 MET cc_start: 0.6012 (mtp) cc_final: 0.5759 (ttp) REVERT: b 111 PHE cc_start: 0.8500 (m-80) cc_final: 0.8105 (m-80) REVERT: b 147 MET cc_start: 0.8130 (mpp) cc_final: 0.6913 (tpt) REVERT: b 245 MET cc_start: 0.8386 (ptp) cc_final: 0.8107 (ptp) REVERT: b 327 MET cc_start: 0.7886 (tmm) cc_final: 0.7538 (tmm) REVERT: b 341 MET cc_start: 0.4320 (mmm) cc_final: 0.3632 (mmm) REVERT: b 396 MET cc_start: 0.8535 (mmm) cc_final: 0.8065 (mmp) REVERT: a 1 MET cc_start: 0.6490 (pmm) cc_final: 0.5453 (ptp) REVERT: a 29 MET cc_start: 0.2828 (ptm) cc_final: 0.2616 (ptm) REVERT: a 245 MET cc_start: 0.8956 (ptp) cc_final: 0.8648 (ptp) REVERT: a 390 MET cc_start: 0.8584 (ptt) cc_final: 0.8212 (ptt) REVERT: d 21 MET cc_start: -0.1872 (mtp) cc_final: -0.2080 (ttp) REVERT: d 29 MET cc_start: 0.7358 (pmm) cc_final: 0.7055 (pmm) REVERT: d 147 MET cc_start: 0.7114 (mmp) cc_final: 0.6482 (tpt) REVERT: d 327 MET cc_start: 0.7420 (ttt) cc_final: 0.6991 (tmm) REVERT: d 341 MET cc_start: 0.1326 (mmp) cc_final: 0.0942 (tpp) REVERT: d 390 MET cc_start: 0.8476 (pmm) cc_final: 0.8213 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3146 time to fit residues: 59.1517 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 : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 195 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 188 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.0870 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 292 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.027504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.021587 restraints weight = 361650.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.022141 restraints weight = 264977.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.022552 restraints weight = 210862.245| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 1.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20401 Z= 0.105 Angle : 0.604 9.447 27503 Z= 0.286 Chirality : 0.042 0.151 3135 Planarity : 0.004 0.048 3525 Dihedral : 9.724 156.715 2917 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 0.99 (0.18), residues: 2490 helix: 1.33 (0.15), residues: 1158 sheet: -0.69 (0.25), residues: 426 loop : 0.70 (0.23), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 381 HIS 0.005 0.001 HIS c 344 PHE 0.023 0.001 PHE e 36 TYR 0.013 0.001 TYR f 332 ARG 0.004 0.000 ARG b 366 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 944) hydrogen bonds : angle 4.31854 ( 2742) covalent geometry : bond 0.00223 (20371) covalent geometry : angle 0.60408 (27503) Misc. bond : bond 0.00291 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.82 seconds wall clock time: 105 minutes 8.21 seconds (6308.21 seconds total)