Starting phenix.real_space_refine on Sat Sep 28 20:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_27914_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_27914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_27914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_27914_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/09_2024/8e5l_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.68, per 1000 atoms: 0.63 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.5 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: 7.03 Time building geometry restraints manager: 6.33 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: 72 2.02 - 2.74: 1654 2.74 - 3.46: 29070 3.46 - 4.18: 46275 4.18 - 4.90: 83659 Nonbonded interactions: 160730 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 3.040 nonbonded pdb=" NH2 ARG b 173 " pdb=" CD ARG a 212 " model vdw 1.352 3.520 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" NH2 ARG b 173 " pdb=" NE ARG a 212 " model vdw 1.392 3.200 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 ... (remaining 160725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.670 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.560 ------------------------------------------------------------------------------- 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 : 0.003 0.087 20371 Z= 0.219 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.189 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: f 21 MET cc_start: 0.1134 (mmm) cc_final: -0.0692 (ttt) REVERT: c 29 MET cc_start: -0.1502 (mtp) cc_final: -0.2173 (ttt) REVERT: b 29 MET cc_start: -0.1529 (mtp) cc_final: -0.2115 (ttt) REVERT: d 21 MET cc_start: -0.0973 (mmm) cc_final: -0.4030 (ttt) outliers start: 35 outliers final: 8 residues processed: 269 average time/residue: 0.3583 time to fit residues: 141.5336 Evaluate side-chains 147 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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: 20.0000 chunk 193 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN c 295 HIS c 340 ASN c 388 HIS 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4645 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 20371 Z= 0.291 Angle : 0.796 9.686 27503 Z= 0.389 Chirality : 0.045 0.174 3135 Planarity : 0.005 0.058 3525 Dihedral : 10.999 147.802 2917 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.19 % Allowed : 2.94 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2490 helix: 0.35 (0.15), residues: 1122 sheet: -0.83 (0.25), residues: 408 loop : 0.27 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 381 HIS 0.009 0.002 HIS c 388 PHE 0.019 0.002 PHE d 355 TYR 0.029 0.002 TYR d 332 ARG 0.013 0.001 ARG c 173 *********************** 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 149 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 2.468 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: e 21 MET cc_start: -0.1951 (ttt) cc_final: -0.2291 (ttt) REVERT: e 341 MET cc_start: 0.1441 (mtp) cc_final: 0.1077 (mtm) REVERT: f 21 MET cc_start: 0.1037 (mmm) cc_final: -0.0260 (mtm) REVERT: c 416 MET cc_start: 0.0831 (ptm) cc_final: 0.0471 (ptt) REVERT: b 396 MET cc_start: 0.4619 (mtt) cc_final: 0.4418 (mtt) REVERT: d 21 MET cc_start: -0.0811 (mmm) cc_final: -0.3270 (mtt) REVERT: d 341 MET cc_start: 0.0390 (tpt) cc_final: -0.0898 (tpt) outliers start: 4 outliers final: 1 residues processed: 149 average time/residue: 0.3084 time to fit residues: 72.6866 Evaluate side-chains 115 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 42 HIS e 126 ASN e 142 ASN ** e 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 0.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20371 Z= 0.313 Angle : 0.796 8.564 27503 Z= 0.396 Chirality : 0.046 0.164 3135 Planarity : 0.005 0.064 3525 Dihedral : 10.844 157.360 2917 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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 (0.16), residues: 2490 helix: -0.09 (0.14), residues: 1170 sheet: -0.88 (0.27), residues: 384 loop : 0.14 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.012 0.002 HIS f 42 PHE 0.047 0.002 PHE f 36 TYR 0.020 0.003 TYR f 332 ARG 0.012 0.001 ARG f 221 *********************** 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 128 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.2389 (ttt) cc_final: -0.2618 (ttt) REVERT: f 21 MET cc_start: 0.2238 (mmm) cc_final: -0.0154 (mtm) REVERT: a 245 MET cc_start: 0.6317 (ptp) cc_final: 0.5076 (ptp) REVERT: d 21 MET cc_start: -0.1066 (mmm) cc_final: -0.2557 (mtt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3234 time to fit residues: 66.1530 Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 238 optimal weight: 0.0070 chunk 117 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 241 GLN ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 239 HIS a 32 GLN a 239 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4885 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20371 Z= 0.159 Angle : 0.602 7.028 27503 Z= 0.291 Chirality : 0.042 0.139 3135 Planarity : 0.003 0.033 3525 Dihedral : 10.439 154.752 2917 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.17), residues: 2490 helix: 0.61 (0.14), residues: 1182 sheet: -1.26 (0.29), residues: 318 loop : 0.58 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 381 HIS 0.005 0.001 HIS c 344 PHE 0.028 0.001 PHE f 36 TYR 0.019 0.002 TYR f 332 ARG 0.005 0.000 ARG c 173 *********************** 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 123 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.309 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: d 21 MET cc_start: -0.0777 (mmm) cc_final: -0.2102 (mtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3165 time to fit residues: 61.7424 Evaluate side-chains 110 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 220 GLN ** 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** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20371 Z= 0.205 Angle : 0.652 9.549 27503 Z= 0.317 Chirality : 0.042 0.139 3135 Planarity : 0.004 0.031 3525 Dihedral : 10.377 159.634 2917 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.39 (0.17), residues: 2490 helix: 0.59 (0.14), residues: 1176 sheet: -0.65 (0.26), residues: 390 loop : 0.52 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.009 0.001 HIS b 344 PHE 0.023 0.002 PHE f 36 TYR 0.012 0.002 TYR d 332 ARG 0.004 0.001 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.419 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: -0.2557 (ttt) cc_final: -0.2787 (ttt) REVERT: b 396 MET cc_start: 0.4980 (mtt) cc_final: 0.4741 (mmm) REVERT: d 21 MET cc_start: -0.0513 (mmm) cc_final: -0.2402 (mtt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3128 time to fit residues: 60.9059 Evaluate side-chains 111 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 moved from start: 0.8193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20371 Z= 0.145 Angle : 0.589 7.289 27503 Z= 0.281 Chirality : 0.041 0.149 3135 Planarity : 0.003 0.030 3525 Dihedral : 10.049 156.204 2917 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2490 helix: 0.94 (0.15), residues: 1182 sheet: -0.68 (0.25), residues: 396 loop : 0.63 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.005 0.001 HIS b 42 PHE 0.014 0.001 PHE f 36 TYR 0.012 0.001 TYR c 332 ARG 0.003 0.000 ARG e 272 *********************** 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 fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.186 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: d 21 MET cc_start: -0.0502 (mmm) cc_final: -0.2248 (mtp) REVERT: d 341 MET cc_start: 0.0622 (tpt) cc_final: 0.0303 (tpt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3050 time to fit residues: 58.7924 Evaluate side-chains 110 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20371 Z= 0.162 Angle : 0.606 8.583 27503 Z= 0.292 Chirality : 0.042 0.157 3135 Planarity : 0.003 0.034 3525 Dihedral : 9.999 160.695 2917 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.17), residues: 2490 helix: 0.96 (0.15), residues: 1176 sheet: -0.98 (0.24), residues: 432 loop : 0.69 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.009 0.001 HIS c 140 PHE 0.010 0.001 PHE f 36 TYR 0.012 0.001 TYR f 332 ARG 0.004 0.000 ARG a 28 *********************** 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 122 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.3094 (ttt) cc_final: -0.3801 (ttt) REVERT: d 21 MET cc_start: -0.0595 (mmm) cc_final: -0.2035 (mtp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3178 time to fit residues: 61.6242 Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 388 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN a 25 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.9174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20371 Z= 0.163 Angle : 0.625 13.120 27503 Z= 0.299 Chirality : 0.042 0.172 3135 Planarity : 0.003 0.037 3525 Dihedral : 9.996 159.536 2917 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2490 helix: 1.00 (0.15), residues: 1176 sheet: -1.04 (0.24), residues: 438 loop : 0.69 (0.24), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 381 HIS 0.013 0.001 HIS e 344 PHE 0.022 0.001 PHE b 335 TYR 0.014 0.001 TYR e 332 ARG 0.003 0.000 ARG e 272 *********************** 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 fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.2858 (ttt) cc_final: -0.3552 (ttt) REVERT: e 341 MET cc_start: 0.0766 (pmm) cc_final: 0.0248 (pmm) REVERT: d 21 MET cc_start: -0.0403 (mmm) cc_final: -0.2078 (mtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3032 time to fit residues: 57.1560 Evaluate side-chains 109 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN f 142 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 292 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 ASN ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 1.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20371 Z= 0.307 Angle : 0.786 11.447 27503 Z= 0.392 Chirality : 0.045 0.216 3135 Planarity : 0.005 0.053 3525 Dihedral : 10.520 163.431 2917 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.05 (0.17), residues: 2490 helix: 0.27 (0.14), residues: 1188 sheet: -1.01 (0.25), residues: 372 loop : 0.50 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.007 0.002 HIS a 344 PHE 0.027 0.002 PHE b 111 TYR 0.029 0.003 TYR f 72 ARG 0.008 0.001 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.445 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: -0.1646 (ttt) cc_final: -0.2143 (ttt) REVERT: e 147 MET cc_start: 0.3240 (mpp) cc_final: 0.2380 (tpp) REVERT: d 21 MET cc_start: -0.0324 (mmm) cc_final: -0.1482 (mtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3153 time to fit residues: 59.3044 Evaluate side-chains 105 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 195 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 0.0010 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 32 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 20 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 120 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 1.0421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20371 Z= 0.141 Angle : 0.619 8.980 27503 Z= 0.296 Chirality : 0.043 0.149 3135 Planarity : 0.003 0.039 3525 Dihedral : 10.017 158.189 2917 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.51 (0.17), residues: 2490 helix: 0.77 (0.15), residues: 1188 sheet: -0.81 (0.25), residues: 426 loop : 0.63 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 381 HIS 0.005 0.001 HIS a 344 PHE 0.028 0.001 PHE b 335 TYR 0.014 0.001 TYR b 72 ARG 0.004 0.000 ARG f 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 119 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 21 MET cc_start: -0.2039 (ttt) cc_final: -0.2250 (ttt) REVERT: d 21 MET cc_start: -0.1046 (mmm) cc_final: -0.2419 (mtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3102 time to fit residues: 59.0903 Evaluate side-chains 107 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.0370 chunk 180 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.7464 ------------------------------------------------------------------------------- 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 ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 241 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.026635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.020780 restraints weight = 370349.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.021314 restraints weight = 275307.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.021699 restraints weight = 220140.485| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 1.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20371 Z= 0.183 Angle : 0.642 10.442 27503 Z= 0.311 Chirality : 0.043 0.219 3135 Planarity : 0.004 0.042 3525 Dihedral : 10.116 160.975 2917 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.48 (0.17), residues: 2490 helix: 0.78 (0.15), residues: 1182 sheet: -0.89 (0.25), residues: 414 loop : 0.59 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 381 HIS 0.006 0.001 HIS c 344 PHE 0.023 0.001 PHE b 335 TYR 0.012 0.001 TYR f 332 ARG 0.007 0.000 ARG c 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.87 seconds wall clock time: 56 minutes 30.97 seconds (3390.97 seconds total)