Starting phenix.real_space_refine on Sat Mar 16 22:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uc2_26442/03_2024/7uc2_26442_updated.pdb" } resolution = 2.5 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= 0.009 sd= 0.193 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 80 5.16 5 C 10008 2.51 5 N 2720 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15820 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "B" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "D" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 8.76, per 1000 atoms: 0.55 Number of scatterers: 15820 At special positions: 0 Unit cell: (92.13, 137.78, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 24 15.00 O 2988 8.00 N 2720 7.00 C 10008 6.00 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.7 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 8 sheets defined 37.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 4.981A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.591A pdb=" N GLN A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.882A pdb=" N LEU A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.752A pdb=" N GLU A 148 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 201 through 204 removed outlier: 3.591A pdb=" N GLY A 204 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.713A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.663A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 455 through 475 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'B' and resid 42 through 57 removed outlier: 5.325A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.592A pdb=" N LYS B 95 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 102 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 201 through 204 removed outlier: 3.627A pdb=" N GLY B 204 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 204' Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.712A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.653A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 455 through 475 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'C' and resid 42 through 57 removed outlier: 5.285A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 77 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 92 through 103 removed outlier: 5.209A pdb=" N LEU C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 102 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 144 through 157 removed outlier: 4.815A pdb=" N GLU C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 206 through 216 removed outlier: 4.667A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 255 through 258 No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.638A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 455 through 475 Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'D' and resid 42 through 57 removed outlier: 5.240A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 77 through 88 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 92 through 103 removed outlier: 5.025A pdb=" N LEU D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 144 through 157 removed outlier: 5.043A pdb=" N GLU D 148 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.642A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.660A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 436 through 446 Processing helix chain 'D' and resid 455 through 475 Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 490 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 7.920A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.910A pdb=" N GLN A 372 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 233 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 370 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 235 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU A 368 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 237 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS A 366 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 393 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 371 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 391 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 373 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A 389 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 196 through 198 removed outlier: 7.899A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 71 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 480 through 483 removed outlier: 6.937A pdb=" N GLN B 372 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 233 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG B 370 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 235 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 368 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 237 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 366 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG B 393 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 371 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 391 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 373 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B 389 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 196 through 198 removed outlier: 7.935A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN C 64 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE C 34 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 66 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE C 36 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 68 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.988A pdb=" N GLN C 372 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 233 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG C 370 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU C 235 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 368 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 237 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS C 366 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG C 393 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 371 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 391 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE C 373 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C 389 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 196 through 198 removed outlier: 7.978A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 480 through 483 removed outlier: 6.907A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 237 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS D 366 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG D 393 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU D 371 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL D 391 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE D 373 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU D 389 " --> pdb=" O PHE D 373 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2585 1.31 - 1.43: 4400 1.43 - 1.56: 9034 1.56 - 1.68: 41 1.68 - 1.81: 132 Bond restraints: 16192 Sorted by residual: bond pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B NAP D 602 " pdb=" C2B NAP D 602 " ideal model delta sigma weight residual 1.528 1.304 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1B NAP B 602 " pdb=" C2B NAP B 602 " ideal model delta sigma weight residual 1.528 1.304 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " ideal model delta sigma weight residual 1.528 1.306 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 16187 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.09: 410 106.09 - 113.16: 8631 113.16 - 120.23: 6002 120.23 - 127.29: 6740 127.29 - 134.36: 197 Bond angle restraints: 21980 Sorted by residual: angle pdb=" N THR C 423 " pdb=" CA THR C 423 " pdb=" C THR C 423 " ideal model delta sigma weight residual 109.72 121.84 -12.12 1.60e+00 3.91e-01 5.74e+01 angle pdb=" N1A NAP D 601 " pdb=" C6A NAP D 601 " pdb=" N6A NAP D 601 " ideal model delta sigma weight residual 119.30 105.48 13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N1A NAP A 602 " pdb=" C6A NAP A 602 " pdb=" N6A NAP A 602 " ideal model delta sigma weight residual 119.30 105.55 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N1A NAP B 602 " pdb=" C6A NAP B 602 " pdb=" N6A NAP B 602 " ideal model delta sigma weight residual 119.30 105.56 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N1A NAP B 601 " pdb=" C6A NAP B 601 " pdb=" N6A NAP B 601 " ideal model delta sigma weight residual 119.30 105.58 13.72 3.00e+00 1.11e-01 2.09e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8092 17.19 - 34.38: 1246 34.38 - 51.57: 473 51.57 - 68.76: 141 68.76 - 85.95: 52 Dihedral angle restraints: 10004 sinusoidal: 4472 harmonic: 5532 Sorted by residual: dihedral pdb=" CA SER D 157 " pdb=" C SER D 157 " pdb=" N CYS D 158 " pdb=" CA CYS D 158 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA C 367 " pdb=" C ALA C 367 " pdb=" N GLU C 368 " pdb=" CA GLU C 368 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER C 157 " pdb=" C SER C 157 " pdb=" N CYS C 158 " pdb=" CA CYS C 158 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2041 0.071 - 0.142: 268 0.142 - 0.214: 8 0.214 - 0.285: 7 0.285 - 0.356: 16 Chirality restraints: 2340 Sorted by residual: chirality pdb=" C2B NAP B 602 " pdb=" C1B NAP B 602 " pdb=" C3B NAP B 602 " pdb=" O2B NAP B 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2B NAP D 602 " pdb=" C1B NAP D 602 " pdb=" C3B NAP D 602 " pdb=" O2B NAP D 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.41 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C2B NAP C 602 " pdb=" C1B NAP C 602 " pdb=" C3B NAP C 602 " pdb=" O2B NAP C 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2337 not shown) Planarity restraints: 2808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 143 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO B 144 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 85 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 86 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 85 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 86 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " 0.027 5.00e-02 4.00e+02 ... (remaining 2805 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1276 2.74 - 3.28: 15498 3.28 - 3.82: 28745 3.82 - 4.36: 35595 4.36 - 4.90: 58528 Nonbonded interactions: 139642 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" OH TYR A 437 " model vdw 2.199 2.440 nonbonded pdb=" O TRP D 462 " pdb=" OG1 THR D 466 " model vdw 2.216 2.440 nonbonded pdb=" O TRP C 462 " pdb=" OG1 THR C 466 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR B 139 " pdb=" OH TYR B 437 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU C 419 " pdb=" OH TYR C 507 " model vdw 2.243 2.440 ... (remaining 139637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.470 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: 2.350 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 43.540 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 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:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.009 0.226 16192 Z= 0.629 Angle : 0.943 13.820 21980 Z= 0.385 Chirality : 0.054 0.356 2340 Planarity : 0.005 0.067 2808 Dihedral : 20.166 85.951 6444 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.02 % Allowed : 23.08 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.65 (0.20), residues: 1884 helix: 1.11 (0.21), residues: 704 sheet: -0.16 (0.26), residues: 416 loop : 0.34 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 53 HIS 0.003 0.001 HIS B 124 PHE 0.015 0.001 PHE B 88 TYR 0.024 0.001 TYR D 249 ARG 0.014 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: B 424 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.4807 (p90) REVERT: C 30 ASP cc_start: 0.7836 (m-30) cc_final: 0.7388 (t0) REVERT: C 424 TYR cc_start: 0.3844 (OUTLIER) cc_final: 0.2220 (t80) outliers start: 17 outliers final: 7 residues processed: 231 average time/residue: 1.3748 time to fit residues: 348.6423 Evaluate side-chains 227 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS C 126 ASN C 133 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16192 Z= 0.358 Angle : 0.606 9.712 21980 Z= 0.312 Chirality : 0.046 0.155 2340 Planarity : 0.006 0.068 2808 Dihedral : 13.359 74.077 2651 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.27 % Allowed : 19.95 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.42 (0.20), residues: 1884 helix: 0.75 (0.20), residues: 700 sheet: -0.40 (0.25), residues: 432 loop : 0.51 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 PHE 0.022 0.002 PHE D 88 TYR 0.023 0.002 TYR C 118 ARG 0.005 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 224 time to evaluate : 1.983 Fit side-chains REVERT: A 47 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7665 (mptm) REVERT: A 81 ARG cc_start: 0.6732 (mtt-85) cc_final: 0.6290 (mmm-85) REVERT: A 282 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7207 (p0) REVERT: B 133 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 282 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6578 (p0) REVERT: B 413 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 424 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.4953 (p90) REVERT: C 252 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: C 424 TYR cc_start: 0.3573 (OUTLIER) cc_final: 0.1961 (t80) REVERT: D 42 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6692 (p0) REVERT: D 413 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7349 (t80) REVERT: D 421 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7866 (m-30) outliers start: 71 outliers final: 26 residues processed: 271 average time/residue: 1.3771 time to fit residues: 410.2202 Evaluate side-chains 255 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 280 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16192 Z= 0.396 Angle : 0.608 9.010 21980 Z= 0.315 Chirality : 0.046 0.138 2340 Planarity : 0.005 0.067 2808 Dihedral : 13.072 59.992 2644 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.05 % Allowed : 19.41 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.19 (0.19), residues: 1884 helix: 0.45 (0.20), residues: 704 sheet: -0.46 (0.25), residues: 428 loop : 0.45 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 PHE 0.019 0.002 PHE D 413 TYR 0.017 0.002 TYR B 118 ARG 0.008 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 219 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7675 (mptm) REVERT: A 182 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (ttm170) REVERT: A 282 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (p0) REVERT: B 282 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6591 (p0) REVERT: B 317 GLU cc_start: 0.7146 (tp30) cc_final: 0.6802 (tp30) REVERT: B 413 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6910 (t80) REVERT: B 419 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: B 424 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.4929 (p90) REVERT: C 347 GLU cc_start: 0.7663 (tt0) cc_final: 0.7429 (tt0) REVERT: C 424 TYR cc_start: 0.3520 (OUTLIER) cc_final: 0.1935 (t80) REVERT: D 133 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7183 (pt0) REVERT: D 297 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: D 421 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7885 (m-30) outliers start: 84 outliers final: 38 residues processed: 274 average time/residue: 1.4020 time to fit residues: 421.0833 Evaluate side-chains 264 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 414 ASN A 451 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16192 Z= 0.153 Angle : 0.502 7.812 21980 Z= 0.261 Chirality : 0.041 0.132 2340 Planarity : 0.004 0.056 2808 Dihedral : 12.129 60.942 2641 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.03 % Allowed : 21.27 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.35 (0.20), residues: 1884 helix: 0.63 (0.21), residues: 704 sheet: -0.43 (0.25), residues: 424 loop : 0.53 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 164 HIS 0.003 0.001 HIS B 201 PHE 0.020 0.001 PHE B 101 TYR 0.015 0.001 TYR B 118 ARG 0.008 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: A 282 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7166 (p0) REVERT: A 511 ASN cc_start: 0.5462 (OUTLIER) cc_final: 0.4915 (m-40) REVERT: B 33 ILE cc_start: 0.8668 (mt) cc_final: 0.8192 (mm) REVERT: B 282 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6472 (p0) REVERT: B 317 GLU cc_start: 0.7137 (tp30) cc_final: 0.6771 (tp30) REVERT: B 413 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6901 (t80) REVERT: B 419 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: B 424 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.4949 (p90) REVERT: C 347 GLU cc_start: 0.7609 (tt0) cc_final: 0.7361 (tt0) REVERT: C 404 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7286 (ppp) REVERT: D 413 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7731 (t80) REVERT: D 421 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7762 (m-30) outliers start: 67 outliers final: 28 residues processed: 264 average time/residue: 1.3356 time to fit residues: 387.7951 Evaluate side-chains 247 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16192 Z= 0.298 Angle : 0.557 8.158 21980 Z= 0.288 Chirality : 0.044 0.143 2340 Planarity : 0.005 0.054 2808 Dihedral : 12.175 60.172 2636 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.69 % Allowed : 20.31 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.25 (0.20), residues: 1884 helix: 0.51 (0.20), residues: 704 sheet: -0.49 (0.25), residues: 428 loop : 0.53 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 164 HIS 0.004 0.001 HIS B 201 PHE 0.024 0.002 PHE B 101 TYR 0.017 0.002 TYR B 118 ARG 0.010 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 213 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7229 (ttm170) REVERT: A 282 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7186 (p0) REVERT: B 119 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7181 (mm-40) REVERT: B 178 GLN cc_start: 0.7305 (mp10) cc_final: 0.7056 (mp-120) REVERT: B 182 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6698 (ttp-110) REVERT: B 282 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6539 (p0) REVERT: B 317 GLU cc_start: 0.7141 (tp30) cc_final: 0.6760 (tp30) REVERT: B 398 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: B 404 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (ppp) REVERT: B 413 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6959 (t80) REVERT: B 419 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 424 TYR cc_start: 0.5677 (OUTLIER) cc_final: 0.4987 (p90) REVERT: C 347 GLU cc_start: 0.7622 (tt0) cc_final: 0.7382 (tt0) REVERT: C 404 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7424 (ppp) REVERT: D 42 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6743 (p0) REVERT: D 297 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: D 413 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7926 (t80) REVERT: D 421 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7795 (m-30) outliers start: 78 outliers final: 35 residues processed: 261 average time/residue: 1.3607 time to fit residues: 390.7601 Evaluate side-chains 261 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.0030 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16192 Z= 0.380 Angle : 0.599 8.905 21980 Z= 0.310 Chirality : 0.046 0.138 2340 Planarity : 0.005 0.067 2808 Dihedral : 12.373 59.845 2636 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.11 % Allowed : 19.95 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.08 (0.19), residues: 1884 helix: 0.31 (0.20), residues: 708 sheet: -0.50 (0.25), residues: 428 loop : 0.43 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 PHE 0.027 0.002 PHE B 101 TYR 0.020 0.002 TYR B 118 ARG 0.012 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 212 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7242 (ttm170) REVERT: A 246 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7081 (ptt-90) REVERT: A 282 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7196 (p0) REVERT: A 357 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7961 (ttp80) REVERT: A 413 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7706 (t80) REVERT: B 119 GLN cc_start: 0.7790 (mm-40) cc_final: 0.6946 (mm110) REVERT: B 182 ARG cc_start: 0.7280 (ttt-90) cc_final: 0.6713 (ttp-110) REVERT: B 282 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6579 (p0) REVERT: B 317 GLU cc_start: 0.7160 (tp30) cc_final: 0.6790 (tp30) REVERT: B 413 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7083 (t80) REVERT: B 419 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: B 424 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4946 (p90) REVERT: C 347 GLU cc_start: 0.7609 (tt0) cc_final: 0.7377 (tt0) REVERT: C 404 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7512 (ppp) REVERT: C 413 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (t80) REVERT: D 42 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6768 (p0) REVERT: D 105 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7794 (t0) REVERT: D 133 GLN cc_start: 0.7363 (pm20) cc_final: 0.7145 (pm20) REVERT: D 297 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: D 398 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: D 413 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8042 (t80) REVERT: D 421 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7841 (m-30) outliers start: 85 outliers final: 43 residues processed: 269 average time/residue: 1.3365 time to fit residues: 395.3398 Evaluate side-chains 264 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 204 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16192 Z= 0.206 Angle : 0.527 8.844 21980 Z= 0.273 Chirality : 0.042 0.133 2340 Planarity : 0.004 0.052 2808 Dihedral : 11.821 59.999 2636 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.51 % Allowed : 21.15 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.22 (0.20), residues: 1884 helix: 0.46 (0.20), residues: 704 sheet: -0.52 (0.25), residues: 428 loop : 0.52 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 164 HIS 0.004 0.001 HIS B 201 PHE 0.027 0.001 PHE B 101 TYR 0.019 0.001 TYR B 118 ARG 0.012 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 2.014 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7202 (ttm170) REVERT: A 282 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7188 (p0) REVERT: A 511 ASN cc_start: 0.5550 (OUTLIER) cc_final: 0.4778 (m110) REVERT: B 33 ILE cc_start: 0.8696 (mt) cc_final: 0.8282 (mm) REVERT: B 119 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7136 (mm-40) REVERT: B 282 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6511 (p0) REVERT: B 317 GLU cc_start: 0.7150 (tp30) cc_final: 0.6776 (tp30) REVERT: B 398 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 413 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 419 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: B 424 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4922 (p90) REVERT: C 347 GLU cc_start: 0.7610 (tt0) cc_final: 0.7366 (tt0) REVERT: D 105 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7799 (t0) REVERT: D 297 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 413 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7729 (t80) outliers start: 75 outliers final: 34 residues processed: 264 average time/residue: 1.3315 time to fit residues: 386.7869 Evaluate side-chains 257 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16192 Z= 0.387 Angle : 0.602 9.092 21980 Z= 0.311 Chirality : 0.046 0.159 2340 Planarity : 0.005 0.069 2808 Dihedral : 12.187 59.850 2636 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.63 % Allowed : 21.03 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.03 (0.19), residues: 1884 helix: 0.26 (0.20), residues: 708 sheet: -0.53 (0.25), residues: 428 loop : 0.42 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 PHE 0.035 0.002 PHE B 101 TYR 0.020 0.002 TYR B 118 ARG 0.013 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 208 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6143 (mmt90) REVERT: A 182 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7240 (ttm170) REVERT: A 282 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7195 (p0) REVERT: A 357 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7935 (ttp80) REVERT: A 413 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7641 (t80) REVERT: B 119 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7114 (mm-40) REVERT: B 182 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.6704 (ttp-110) REVERT: B 282 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6570 (p0) REVERT: B 317 GLU cc_start: 0.7162 (tp30) cc_final: 0.6787 (tp30) REVERT: B 398 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: B 413 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 419 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: B 424 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.4945 (p90) REVERT: C 88 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.4745 (m-80) REVERT: C 119 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: C 347 GLU cc_start: 0.7611 (tt0) cc_final: 0.7388 (tt0) REVERT: D 105 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7823 (t0) REVERT: D 297 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: D 398 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: D 413 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8041 (t80) REVERT: D 421 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7856 (m-30) outliers start: 77 outliers final: 41 residues processed: 259 average time/residue: 1.3694 time to fit residues: 389.6872 Evaluate side-chains 262 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16192 Z= 0.240 Angle : 0.540 9.201 21980 Z= 0.280 Chirality : 0.043 0.150 2340 Planarity : 0.005 0.055 2808 Dihedral : 11.789 59.990 2636 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.67 % Allowed : 22.18 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.15 (0.20), residues: 1884 helix: 0.39 (0.20), residues: 704 sheet: -0.52 (0.25), residues: 428 loop : 0.49 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 164 HIS 0.004 0.001 HIS B 201 PHE 0.039 0.001 PHE B 101 TYR 0.020 0.001 TYR B 118 ARG 0.011 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6156 (mmt90) REVERT: A 182 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: A 282 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7175 (p0) REVERT: B 119 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7108 (mm-40) REVERT: B 260 MET cc_start: 0.8861 (ttm) cc_final: 0.8607 (mtt) REVERT: B 282 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6510 (p0) REVERT: B 317 GLU cc_start: 0.7149 (tp30) cc_final: 0.6789 (tp30) REVERT: B 413 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7044 (t80) REVERT: B 419 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: B 424 TYR cc_start: 0.5646 (OUTLIER) cc_final: 0.4922 (p90) REVERT: C 85 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7190 (mm-30) REVERT: C 88 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.4753 (m-80) REVERT: C 119 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7927 (tp40) REVERT: C 347 GLU cc_start: 0.7604 (tt0) cc_final: 0.7370 (tt0) REVERT: D 105 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7844 (t0) REVERT: D 297 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: D 413 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7786 (t80) REVERT: D 421 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7809 (m-30) outliers start: 61 outliers final: 43 residues processed: 258 average time/residue: 1.3021 time to fit residues: 370.2326 Evaluate side-chains 266 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 187 optimal weight: 0.0040 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 155 HIS C 178 GLN D 83 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16192 Z= 0.174 Angle : 0.519 9.282 21980 Z= 0.268 Chirality : 0.042 0.143 2340 Planarity : 0.004 0.052 2808 Dihedral : 11.481 59.337 2636 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.31 % Allowed : 22.54 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.23 (0.20), residues: 1884 helix: 0.47 (0.20), residues: 704 sheet: -0.47 (0.25), residues: 424 loop : 0.49 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 164 HIS 0.003 0.001 HIS B 186 PHE 0.043 0.001 PHE B 101 TYR 0.018 0.001 TYR B 118 ARG 0.012 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 212 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7373 (mt0) cc_final: 0.7162 (mt0) REVERT: A 182 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7176 (ttm170) REVERT: A 282 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7168 (p0) REVERT: B 33 ILE cc_start: 0.8662 (mt) cc_final: 0.8205 (mm) REVERT: B 119 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7081 (mm-40) REVERT: B 282 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6475 (p0) REVERT: B 317 GLU cc_start: 0.7114 (tp30) cc_final: 0.6757 (tp30) REVERT: B 413 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6968 (t80) REVERT: B 419 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: B 424 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4918 (p90) REVERT: C 347 GLU cc_start: 0.7624 (tt0) cc_final: 0.7382 (tt0) REVERT: D 297 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: D 413 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 421 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7767 (m-30) outliers start: 55 outliers final: 34 residues processed: 249 average time/residue: 1.3103 time to fit residues: 360.0829 Evaluate side-chains 249 residues out of total 1664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 178 GLN D 83 GLN D 105 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102241 restraints weight = 19034.700| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.71 r_work: 0.3095 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16192 Z= 0.258 Angle : 0.547 9.317 21980 Z= 0.283 Chirality : 0.043 0.194 2340 Planarity : 0.005 0.052 2808 Dihedral : 11.603 58.894 2636 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.00 % Allowed : 23.02 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.16 (0.20), residues: 1884 helix: 0.39 (0.20), residues: 708 sheet: -0.50 (0.25), residues: 428 loop : 0.50 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 53 HIS 0.003 0.001 HIS B 186 PHE 0.043 0.002 PHE B 101 TYR 0.019 0.001 TYR B 118 ARG 0.011 0.000 ARG C 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6083.91 seconds wall clock time: 108 minutes 5.48 seconds (6485.48 seconds total)