Starting phenix.real_space_refine on Wed Mar 4 14:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plw_20378/03_2026/6plw_20378.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9180 2.51 5 N 2265 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14095 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.23 Number of scatterers: 14095 At special positions: 0 Unit cell: (106.99, 105.344, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2560 8.00 N 2265 7.00 C 9180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 605.1 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 39.3% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.577A pdb=" N PHE A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.881A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.722A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.577A pdb=" N PHE B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.881A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.194A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.577A pdb=" N PHE C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.016A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 400 " --> pdb=" O ILE D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.577A pdb=" N PHE D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.674A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 285 removed outlier: 3.822A pdb=" N LEU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.577A pdb=" N PHE E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.504A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.504A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 6.271A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 720 hydrogen bonds defined for protein. 2070 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: 2.34 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4350 1.35 - 1.47: 3927 1.47 - 1.60: 6013 1.60 - 1.73: 0 1.73 - 1.86: 150 Bond restraints: 14440 Sorted by residual: bond pdb=" CB ARG A 234 " pdb=" CG ARG A 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG E 234 " pdb=" CG ARG E 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.69e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" CB ARG C 234 " pdb=" CG ARG C 234 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.57e+00 ... (remaining 14435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 19037 2.60 - 5.19: 487 5.19 - 7.79: 71 7.79 - 10.39: 10 10.39 - 12.99: 5 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 134.49 -12.95 1.91e+00 2.74e-01 4.60e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 8531 21.59 - 43.18: 194 43.18 - 64.77: 25 64.77 - 86.36: 35 86.36 - 107.95: 20 Dihedral angle restraints: 8805 sinusoidal: 3690 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 ... (remaining 8802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1606 0.059 - 0.118: 541 0.118 - 0.177: 88 0.177 - 0.236: 19 0.236 - 0.295: 6 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR B 128 " -0.040 2.00e-02 2.50e+03 pdb=" O THR B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 128 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR E 128 " 0.040 2.00e-02 2.50e+03 pdb=" O THR E 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR E 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 128 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4128 2.80 - 3.33: 12273 3.33 - 3.85: 23354 3.85 - 4.38: 27386 4.38 - 4.90: 45549 Nonbonded interactions: 112690 Sorted by model distance: nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.277 3.040 ... (remaining 112685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.010 0.065 14465 Z= 0.437 Angle : 1.027 12.987 19675 Z= 0.528 Chirality : 0.060 0.295 2260 Planarity : 0.007 0.047 2435 Dihedral : 13.315 107.951 5455 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.15), residues: 1710 helix: -4.53 (0.10), residues: 600 sheet: -1.36 (0.24), residues: 345 loop : -2.80 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 407 TYR 0.026 0.003 TYR C 425 PHE 0.023 0.003 PHE B 115 TRP 0.022 0.003 TRP D 110 HIS 0.006 0.002 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00997 (14440) covalent geometry : angle 1.01745 (19610) SS BOND : bond 0.00711 ( 10) SS BOND : angle 3.38826 ( 20) hydrogen bonds : bond 0.28279 ( 575) hydrogen bonds : angle 9.40116 ( 2070) link_BETA1-4 : bond 0.00322 ( 10) link_BETA1-4 : angle 2.29120 ( 30) link_NAG-ASN : bond 0.00745 ( 5) link_NAG-ASN : angle 1.93356 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8392 (ttp) cc_final: 0.7531 (ttt) REVERT: A 28 GLU cc_start: 0.8966 (tp30) cc_final: 0.8747 (tm-30) REVERT: A 105 MET cc_start: 0.8435 (mmp) cc_final: 0.8130 (mpp) REVERT: A 249 LEU cc_start: 0.9356 (mt) cc_final: 0.9012 (pp) REVERT: A 317 TYR cc_start: 0.8371 (t80) cc_final: 0.7818 (t80) REVERT: B 173 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 249 LEU cc_start: 0.9329 (mt) cc_final: 0.8999 (pp) REVERT: C 105 MET cc_start: 0.8458 (mmp) cc_final: 0.8231 (mpp) REVERT: C 249 LEU cc_start: 0.9315 (mt) cc_final: 0.9031 (pp) REVERT: D 72 MET cc_start: 0.8996 (mtm) cc_final: 0.8754 (mtm) REVERT: D 173 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7616 (mm-30) REVERT: D 249 LEU cc_start: 0.9290 (mt) cc_final: 0.8993 (pp) REVERT: D 292 LYS cc_start: 0.9260 (mttt) cc_final: 0.9004 (mmmm) REVERT: D 317 TYR cc_start: 0.8351 (t80) cc_final: 0.8087 (t80) REVERT: E 249 LEU cc_start: 0.9299 (mt) cc_final: 0.8934 (pp) REVERT: E 416 ILE cc_start: 0.9509 (tp) cc_final: 0.9292 (tp) outliers start: 0 outliers final: 2 residues processed: 322 average time/residue: 0.6154 time to fit residues: 216.2680 Evaluate side-chains 177 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain E residue 258 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 82 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 77 ASN B 82 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 82 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 77 ASN D 82 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 82 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062337 restraints weight = 34072.988| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.67 r_work: 0.2797 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14465 Z= 0.146 Angle : 0.732 10.920 19675 Z= 0.365 Chirality : 0.045 0.200 2260 Planarity : 0.005 0.051 2435 Dihedral : 11.163 67.868 2199 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.65 % Allowed : 10.33 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.17), residues: 1710 helix: -2.78 (0.16), residues: 615 sheet: -0.72 (0.26), residues: 345 loop : -2.39 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 75 TYR 0.017 0.001 TYR B 238 PHE 0.022 0.001 PHE D 258 TRP 0.008 0.001 TRP A 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00313 (14440) covalent geometry : angle 0.72382 (19610) SS BOND : bond 0.00604 ( 10) SS BOND : angle 1.66719 ( 20) hydrogen bonds : bond 0.04893 ( 575) hydrogen bonds : angle 5.17244 ( 2070) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 2.63775 ( 30) link_NAG-ASN : bond 0.00030 ( 5) link_NAG-ASN : angle 0.81844 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7844 (mm-40) REVERT: A 173 GLU cc_start: 0.8219 (mp0) cc_final: 0.7811 (mm-30) REVERT: A 241 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (mp) REVERT: A 300 ASP cc_start: 0.9295 (m-30) cc_final: 0.8984 (m-30) REVERT: B 28 GLU cc_start: 0.8378 (mp0) cc_final: 0.8058 (mp0) REVERT: B 43 ARG cc_start: 0.9559 (mtm-85) cc_final: 0.9137 (mtm-85) REVERT: B 173 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8153 (mm-30) REVERT: B 235 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9095 (mm110) REVERT: B 243 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8509 (mmm) REVERT: B 300 ASP cc_start: 0.9266 (m-30) cc_final: 0.8926 (m-30) REVERT: B 317 TYR cc_start: 0.8621 (t80) cc_final: 0.8306 (t80) REVERT: C 43 ARG cc_start: 0.9560 (mtm-85) cc_final: 0.9341 (mtm180) REVERT: C 105 MET cc_start: 0.9053 (mmp) cc_final: 0.8844 (mmp) REVERT: C 243 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: C 300 ASP cc_start: 0.9259 (m-30) cc_final: 0.8942 (m-30) REVERT: C 317 TYR cc_start: 0.8538 (t80) cc_final: 0.8084 (t80) REVERT: D 72 MET cc_start: 0.9254 (mtm) cc_final: 0.8951 (mmm) REVERT: D 105 MET cc_start: 0.9088 (mmp) cc_final: 0.8836 (mmp) REVERT: D 173 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8044 (mm-30) REVERT: D 235 GLN cc_start: 0.9301 (mm-40) cc_final: 0.9060 (mm110) REVERT: D 243 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8519 (mmm) REVERT: D 391 MET cc_start: 0.0195 (tpt) cc_final: -0.0086 (tpp) REVERT: E 243 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8728 (mmm) REVERT: E 300 ASP cc_start: 0.9258 (m-30) cc_final: 0.8963 (m-30) REVERT: E 317 TYR cc_start: 0.8561 (t80) cc_final: 0.8301 (t80) REVERT: E 391 MET cc_start: 0.0498 (tpt) cc_final: 0.0150 (tpp) outliers start: 40 outliers final: 13 residues processed: 250 average time/residue: 0.4921 time to fit residues: 137.0070 Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 4 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 231 HIS B 77 ASN B 166 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 62 ASN C 77 ASN C 231 HIS D 62 ASN D 77 ASN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS E 231 HIS ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060258 restraints weight = 34040.321| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.80 r_work: 0.2683 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14465 Z= 0.211 Angle : 0.695 9.080 19675 Z= 0.347 Chirality : 0.045 0.151 2260 Planarity : 0.004 0.045 2435 Dihedral : 8.306 58.651 2195 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.91 % Allowed : 10.86 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.19), residues: 1710 helix: -1.71 (0.19), residues: 615 sheet: -0.23 (0.28), residues: 345 loop : -1.76 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 75 TYR 0.012 0.002 TYR E 144 PHE 0.011 0.001 PHE D 258 TRP 0.009 0.001 TRP D 186 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00477 (14440) covalent geometry : angle 0.68320 (19610) SS BOND : bond 0.00734 ( 10) SS BOND : angle 2.30399 ( 20) hydrogen bonds : bond 0.04174 ( 575) hydrogen bonds : angle 4.70796 ( 2070) link_BETA1-4 : bond 0.00428 ( 10) link_BETA1-4 : angle 2.68472 ( 30) link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 1.12960 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8395 (mp0) cc_final: 0.8077 (mp0) REVERT: A 105 MET cc_start: 0.9219 (mmm) cc_final: 0.8996 (mmm) REVERT: A 156 MET cc_start: 0.9240 (mmm) cc_final: 0.8999 (mmm) REVERT: A 243 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8747 (mmm) REVERT: A 300 ASP cc_start: 0.9392 (m-30) cc_final: 0.9044 (m-30) REVERT: A 317 TYR cc_start: 0.8594 (t80) cc_final: 0.8362 (t80) REVERT: B 43 ARG cc_start: 0.9393 (mtm-85) cc_final: 0.9182 (mtm-85) REVERT: B 75 ARG cc_start: 0.9006 (ttm110) cc_final: 0.8759 (mtp-110) REVERT: B 156 MET cc_start: 0.9376 (mmt) cc_final: 0.9010 (mmt) REVERT: B 173 GLU cc_start: 0.8782 (mt-10) cc_final: 0.7945 (mp0) REVERT: B 241 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 243 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8417 (mpp) REVERT: B 262 MET cc_start: 0.7198 (mpt) cc_final: 0.6968 (pmm) REVERT: B 306 CYS cc_start: 0.8736 (m) cc_final: 0.8210 (t) REVERT: B 317 TYR cc_start: 0.8653 (t80) cc_final: 0.8414 (t80) REVERT: B 420 PHE cc_start: 0.8754 (m-80) cc_final: 0.8547 (m-80) REVERT: C 72 MET cc_start: 0.9190 (mtm) cc_final: 0.8973 (mmm) REVERT: C 105 MET cc_start: 0.9208 (mmp) cc_final: 0.8962 (mmp) REVERT: C 163 MET cc_start: 0.8800 (mpp) cc_final: 0.8130 (mtp) REVERT: C 173 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: C 235 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9160 (mm-40) REVERT: C 243 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8568 (mmm) REVERT: C 300 ASP cc_start: 0.9347 (m-30) cc_final: 0.9007 (m-30) REVERT: C 306 CYS cc_start: 0.8612 (m) cc_final: 0.8288 (t) REVERT: C 317 TYR cc_start: 0.8573 (t80) cc_final: 0.8354 (t80) REVERT: D 72 MET cc_start: 0.9260 (mtm) cc_final: 0.9029 (mtm) REVERT: D 75 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8785 (mtp-110) REVERT: D 173 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8063 (mp0) REVERT: D 243 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: D 262 MET cc_start: 0.7323 (mpt) cc_final: 0.7052 (pmm) REVERT: D 300 ASP cc_start: 0.9332 (m-30) cc_final: 0.8937 (m-30) REVERT: D 317 TYR cc_start: 0.8555 (t80) cc_final: 0.8304 (t80) REVERT: E 28 GLU cc_start: 0.8574 (mp0) cc_final: 0.8205 (mp0) REVERT: E 72 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9086 (mmt) REVERT: E 243 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8717 (mmm) REVERT: E 262 MET cc_start: 0.7170 (mmt) cc_final: 0.6958 (mpm) REVERT: E 300 ASP cc_start: 0.9355 (m-30) cc_final: 0.9024 (m-30) REVERT: E 317 TYR cc_start: 0.8582 (t80) cc_final: 0.8379 (t80) REVERT: E 391 MET cc_start: 0.0840 (tpt) cc_final: 0.0558 (tpp) outliers start: 44 outliers final: 19 residues processed: 215 average time/residue: 0.4563 time to fit residues: 109.7918 Evaluate side-chains 196 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060005 restraints weight = 34427.317| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.83 r_work: 0.2669 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14465 Z= 0.211 Angle : 0.674 10.125 19675 Z= 0.336 Chirality : 0.045 0.187 2260 Planarity : 0.004 0.059 2435 Dihedral : 6.617 53.039 2195 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.38 % Allowed : 11.79 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1710 helix: -1.09 (0.20), residues: 620 sheet: 0.15 (0.30), residues: 345 loop : -1.62 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.012 0.002 TYR D 144 PHE 0.010 0.001 PHE A 258 TRP 0.009 0.001 TRP D 259 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00479 (14440) covalent geometry : angle 0.66366 (19610) SS BOND : bond 0.00510 ( 10) SS BOND : angle 2.24468 ( 20) hydrogen bonds : bond 0.03717 ( 575) hydrogen bonds : angle 4.47025 ( 2070) link_BETA1-4 : bond 0.00380 ( 10) link_BETA1-4 : angle 2.46025 ( 30) link_NAG-ASN : bond 0.00220 ( 5) link_NAG-ASN : angle 0.97992 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 243 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8438 (mpp) REVERT: A 300 ASP cc_start: 0.9369 (m-30) cc_final: 0.9020 (m-30) REVERT: A 306 CYS cc_start: 0.8788 (m) cc_final: 0.8273 (t) REVERT: B 71 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9278 (p) REVERT: B 72 MET cc_start: 0.9259 (mtm) cc_final: 0.8862 (mmt) REVERT: B 75 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8786 (mtp-110) REVERT: B 166 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8158 (tp40) REVERT: B 173 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8043 (mm-30) REVERT: B 241 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 243 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8406 (mpp) REVERT: B 262 MET cc_start: 0.7140 (mpt) cc_final: 0.6940 (pmm) REVERT: B 300 ASP cc_start: 0.9349 (m-30) cc_final: 0.8954 (m-30) REVERT: B 306 CYS cc_start: 0.8716 (m) cc_final: 0.8265 (t) REVERT: B 420 PHE cc_start: 0.8793 (m-80) cc_final: 0.8587 (m-80) REVERT: C 235 GLN cc_start: 0.9387 (mm-40) cc_final: 0.9177 (mm-40) REVERT: C 242 GLN cc_start: 0.8536 (tp40) cc_final: 0.8288 (tm-30) REVERT: C 243 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8541 (mmm) REVERT: C 300 ASP cc_start: 0.9327 (m-30) cc_final: 0.8991 (m-30) REVERT: C 306 CYS cc_start: 0.8616 (m) cc_final: 0.8292 (t) REVERT: C 317 TYR cc_start: 0.8644 (t80) cc_final: 0.8440 (t80) REVERT: D 75 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8799 (mtp-110) REVERT: D 105 MET cc_start: 0.9233 (mmp) cc_final: 0.8957 (mmp) REVERT: D 173 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7934 (mp0) REVERT: D 235 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9079 (mm110) REVERT: D 242 GLN cc_start: 0.8815 (tp40) cc_final: 0.8358 (tm-30) REVERT: D 243 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: D 262 MET cc_start: 0.7320 (mpt) cc_final: 0.7057 (pmm) REVERT: D 300 ASP cc_start: 0.9294 (m-30) cc_final: 0.8886 (m-30) REVERT: D 317 TYR cc_start: 0.8633 (t80) cc_final: 0.8418 (t80) REVERT: E 28 GLU cc_start: 0.8568 (mp0) cc_final: 0.8356 (mp0) REVERT: E 72 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8987 (mmt) REVERT: E 243 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8671 (mmm) REVERT: E 262 MET cc_start: 0.7193 (mmt) cc_final: 0.6713 (pmm) REVERT: E 300 ASP cc_start: 0.9344 (m-30) cc_final: 0.9028 (m-30) REVERT: E 306 CYS cc_start: 0.8612 (m) cc_final: 0.8266 (t) outliers start: 51 outliers final: 19 residues processed: 212 average time/residue: 0.4584 time to fit residues: 109.4197 Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060461 restraints weight = 34901.223| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.78 r_work: 0.2732 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14465 Z= 0.184 Angle : 0.656 9.575 19675 Z= 0.327 Chirality : 0.045 0.205 2260 Planarity : 0.004 0.059 2435 Dihedral : 6.021 43.945 2195 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.65 % Allowed : 14.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1710 helix: -0.61 (0.21), residues: 600 sheet: 0.28 (0.30), residues: 345 loop : -1.33 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.025 0.002 TYR B 317 PHE 0.011 0.001 PHE E 258 TRP 0.009 0.001 TRP D 259 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00417 (14440) covalent geometry : angle 0.64671 (19610) SS BOND : bond 0.00612 ( 10) SS BOND : angle 2.41098 ( 20) hydrogen bonds : bond 0.03617 ( 575) hydrogen bonds : angle 4.33518 ( 2070) link_BETA1-4 : bond 0.00349 ( 10) link_BETA1-4 : angle 2.07105 ( 30) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 0.85687 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9273 (mmm) cc_final: 0.8533 (mpm) REVERT: A 241 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8861 (mp) REVERT: A 243 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8452 (mpp) REVERT: A 300 ASP cc_start: 0.9323 (m-30) cc_final: 0.8969 (m-30) REVERT: A 306 CYS cc_start: 0.8736 (m) cc_final: 0.8319 (t) REVERT: A 317 TYR cc_start: 0.8544 (t80) cc_final: 0.8279 (t80) REVERT: B 71 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9275 (p) REVERT: B 72 MET cc_start: 0.9232 (mtm) cc_final: 0.8864 (mmt) REVERT: B 75 ARG cc_start: 0.9086 (ttm110) cc_final: 0.8836 (mtp-110) REVERT: B 166 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8404 (tp40) REVERT: B 173 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8134 (mm-30) REVERT: B 241 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 243 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: B 300 ASP cc_start: 0.9322 (m-30) cc_final: 0.8927 (m-30) REVERT: B 306 CYS cc_start: 0.8705 (m) cc_final: 0.8256 (t) REVERT: B 317 TYR cc_start: 0.8305 (t80) cc_final: 0.8011 (t80) REVERT: C 105 MET cc_start: 0.8866 (mmm) cc_final: 0.8618 (mmp) REVERT: C 163 MET cc_start: 0.8714 (mpp) cc_final: 0.8291 (mtp) REVERT: C 202 GLN cc_start: 0.9178 (mt0) cc_final: 0.8761 (mp10) REVERT: C 243 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8375 (mpp) REVERT: C 300 ASP cc_start: 0.9298 (m-30) cc_final: 0.8970 (m-30) REVERT: C 306 CYS cc_start: 0.8676 (m) cc_final: 0.8320 (t) REVERT: C 317 TYR cc_start: 0.8642 (t80) cc_final: 0.8436 (t80) REVERT: D 31 ASP cc_start: 0.9124 (m-30) cc_final: 0.8586 (m-30) REVERT: D 75 ARG cc_start: 0.9089 (ttm110) cc_final: 0.8843 (mtp-110) REVERT: D 156 MET cc_start: 0.9270 (mmm) cc_final: 0.9007 (mmm) REVERT: D 166 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8267 (mm-40) REVERT: D 173 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8131 (mm-30) REVERT: D 241 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8855 (mp) REVERT: D 242 GLN cc_start: 0.8826 (tp40) cc_final: 0.8458 (tm-30) REVERT: D 243 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8533 (mpp) REVERT: D 262 MET cc_start: 0.7290 (mpt) cc_final: 0.7050 (pmm) REVERT: D 292 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9205 (mtmm) REVERT: D 300 ASP cc_start: 0.9259 (m-30) cc_final: 0.8858 (m-30) REVERT: D 391 MET cc_start: 0.0352 (tpt) cc_final: -0.0045 (tpp) REVERT: D 420 PHE cc_start: 0.8716 (m-80) cc_final: 0.8472 (m-80) REVERT: E 72 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9006 (mmt) REVERT: E 243 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (mmm) REVERT: E 300 ASP cc_start: 0.9271 (m-30) cc_final: 0.8974 (m-30) REVERT: E 306 CYS cc_start: 0.8722 (m) cc_final: 0.8343 (t) REVERT: E 317 TYR cc_start: 0.8567 (t80) cc_final: 0.8354 (t80) outliers start: 40 outliers final: 23 residues processed: 206 average time/residue: 0.4996 time to fit residues: 114.9779 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060696 restraints weight = 34620.622| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.79 r_work: 0.2696 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14465 Z= 0.172 Angle : 0.670 9.329 19675 Z= 0.333 Chirality : 0.045 0.211 2260 Planarity : 0.004 0.059 2435 Dihedral : 5.738 33.750 2195 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.11 % Allowed : 14.90 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1710 helix: -0.38 (0.21), residues: 600 sheet: 0.34 (0.30), residues: 345 loop : -1.27 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.020 0.001 TYR B 317 PHE 0.011 0.001 PHE E 258 TRP 0.008 0.001 TRP E 259 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00394 (14440) covalent geometry : angle 0.66274 (19610) SS BOND : bond 0.00477 ( 10) SS BOND : angle 2.30623 ( 20) hydrogen bonds : bond 0.03554 ( 575) hydrogen bonds : angle 4.22890 ( 2070) link_BETA1-4 : bond 0.00333 ( 10) link_BETA1-4 : angle 1.85099 ( 30) link_NAG-ASN : bond 0.00151 ( 5) link_NAG-ASN : angle 0.81267 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8445 (ptm) cc_final: 0.8213 (tmt) REVERT: A 241 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 243 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8446 (mpp) REVERT: A 300 ASP cc_start: 0.9325 (m-30) cc_final: 0.8972 (m-30) REVERT: A 306 CYS cc_start: 0.8648 (m) cc_final: 0.8312 (t) REVERT: A 317 TYR cc_start: 0.8638 (t80) cc_final: 0.8411 (t80) REVERT: B 71 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9239 (p) REVERT: B 72 MET cc_start: 0.9222 (mtm) cc_final: 0.8838 (mmt) REVERT: B 75 ARG cc_start: 0.9086 (ttm110) cc_final: 0.8821 (mtp-110) REVERT: B 105 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8537 (mpp) REVERT: B 173 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8071 (mp0) REVERT: B 241 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 243 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8318 (mpp) REVERT: B 300 ASP cc_start: 0.9332 (m-30) cc_final: 0.8930 (m-30) REVERT: B 306 CYS cc_start: 0.8634 (m) cc_final: 0.8276 (t) REVERT: B 317 TYR cc_start: 0.8398 (t80) cc_final: 0.8106 (t80) REVERT: C 163 MET cc_start: 0.8685 (mpp) cc_final: 0.8242 (mtp) REVERT: C 202 GLN cc_start: 0.9178 (mt0) cc_final: 0.8765 (mp10) REVERT: C 243 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: C 300 ASP cc_start: 0.9309 (m-30) cc_final: 0.8969 (m-30) REVERT: C 306 CYS cc_start: 0.8579 (m) cc_final: 0.8298 (t) REVERT: C 317 TYR cc_start: 0.8649 (t80) cc_final: 0.8445 (t80) REVERT: D 72 MET cc_start: 0.9230 (mtm) cc_final: 0.8753 (mmm) REVERT: D 75 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8809 (mtp-110) REVERT: D 107 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8887 (p0) REVERT: D 173 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8073 (mm-30) REVERT: D 241 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8807 (mp) REVERT: D 242 GLN cc_start: 0.8835 (tp40) cc_final: 0.8460 (tm-30) REVERT: D 243 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8526 (mpp) REVERT: D 292 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9173 (mtmm) REVERT: D 300 ASP cc_start: 0.9261 (m-30) cc_final: 0.8853 (m-30) REVERT: D 306 CYS cc_start: 0.8740 (m) cc_final: 0.8499 (t) REVERT: D 317 TYR cc_start: 0.8580 (t80) cc_final: 0.8302 (t80) REVERT: D 391 MET cc_start: 0.0471 (tpt) cc_final: 0.0155 (tpp) REVERT: D 420 PHE cc_start: 0.8750 (m-80) cc_final: 0.8516 (m-80) REVERT: E 72 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.9014 (mmt) REVERT: E 243 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8660 (mmm) REVERT: E 300 ASP cc_start: 0.9297 (m-30) cc_final: 0.8991 (m-30) REVERT: E 306 CYS cc_start: 0.8707 (m) cc_final: 0.8363 (t) REVERT: E 317 TYR cc_start: 0.8518 (t80) cc_final: 0.8318 (t80) outliers start: 47 outliers final: 24 residues processed: 202 average time/residue: 0.4973 time to fit residues: 112.4090 Evaluate side-chains 206 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 166 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061375 restraints weight = 34030.903| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.83 r_work: 0.2701 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14465 Z= 0.138 Angle : 0.645 9.558 19675 Z= 0.321 Chirality : 0.045 0.196 2260 Planarity : 0.004 0.065 2435 Dihedral : 5.445 24.356 2195 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.72 % Allowed : 15.63 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1710 helix: -0.24 (0.21), residues: 600 sheet: 0.41 (0.30), residues: 345 loop : -1.22 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.019 0.001 TYR B 317 PHE 0.012 0.001 PHE E 258 TRP 0.008 0.001 TRP E 259 HIS 0.001 0.000 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00316 (14440) covalent geometry : angle 0.64019 (19610) SS BOND : bond 0.00427 ( 10) SS BOND : angle 1.89818 ( 20) hydrogen bonds : bond 0.03446 ( 575) hydrogen bonds : angle 4.08246 ( 2070) link_BETA1-4 : bond 0.00339 ( 10) link_BETA1-4 : angle 1.63545 ( 30) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 0.71210 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9289 (mmm) cc_final: 0.8920 (mmt) REVERT: A 156 MET cc_start: 0.9139 (mtp) cc_final: 0.8928 (tpp) REVERT: A 202 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8669 (mm110) REVERT: A 241 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 243 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8413 (mpp) REVERT: A 300 ASP cc_start: 0.9313 (m-30) cc_final: 0.8973 (m-30) REVERT: A 306 CYS cc_start: 0.8589 (m) cc_final: 0.8303 (t) REVERT: A 317 TYR cc_start: 0.8636 (t80) cc_final: 0.8409 (t80) REVERT: B 71 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9222 (p) REVERT: B 72 MET cc_start: 0.9172 (mtm) cc_final: 0.8900 (mmm) REVERT: B 156 MET cc_start: 0.9342 (mmt) cc_final: 0.8854 (mmt) REVERT: B 173 GLU cc_start: 0.8682 (mt-10) cc_final: 0.7845 (mp0) REVERT: B 241 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8743 (mp) REVERT: B 243 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8354 (mpp) REVERT: B 300 ASP cc_start: 0.9340 (m-30) cc_final: 0.8941 (m-30) REVERT: B 306 CYS cc_start: 0.8613 (m) cc_final: 0.8267 (t) REVERT: B 317 TYR cc_start: 0.8405 (t80) cc_final: 0.8122 (t80) REVERT: C 156 MET cc_start: 0.9197 (tpp) cc_final: 0.8888 (tpp) REVERT: C 163 MET cc_start: 0.8602 (mpp) cc_final: 0.8161 (mtp) REVERT: C 202 GLN cc_start: 0.9172 (mt0) cc_final: 0.8749 (mp10) REVERT: C 243 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8385 (mmm) REVERT: C 300 ASP cc_start: 0.9291 (m-30) cc_final: 0.8942 (m-30) REVERT: C 306 CYS cc_start: 0.8508 (m) cc_final: 0.8271 (t) REVERT: D 31 ASP cc_start: 0.9093 (m-30) cc_final: 0.8536 (m-30) REVERT: D 72 MET cc_start: 0.9210 (mtm) cc_final: 0.8920 (mmm) REVERT: D 75 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8807 (mtp-110) REVERT: D 107 ASP cc_start: 0.9286 (t0) cc_final: 0.8942 (p0) REVERT: D 156 MET cc_start: 0.9055 (mmm) cc_final: 0.8685 (tpp) REVERT: D 173 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7981 (mm-30) REVERT: D 242 GLN cc_start: 0.8820 (tp40) cc_final: 0.8513 (tm-30) REVERT: D 243 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: D 292 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9169 (mtmm) REVERT: D 300 ASP cc_start: 0.9270 (m-30) cc_final: 0.8867 (m-30) REVERT: D 317 TYR cc_start: 0.8575 (t80) cc_final: 0.8294 (t80) REVERT: D 391 MET cc_start: 0.0503 (tpt) cc_final: 0.0261 (tpp) REVERT: D 420 PHE cc_start: 0.8746 (m-80) cc_final: 0.8514 (m-80) REVERT: E 72 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9010 (mmt) REVERT: E 156 MET cc_start: 0.9511 (tpp) cc_final: 0.9178 (mmt) REVERT: E 202 GLN cc_start: 0.9196 (mt0) cc_final: 0.8868 (mm-40) REVERT: E 243 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8673 (mmm) REVERT: E 300 ASP cc_start: 0.9307 (m-30) cc_final: 0.9015 (m-30) REVERT: E 306 CYS cc_start: 0.8579 (m) cc_final: 0.8297 (t) outliers start: 41 outliers final: 23 residues processed: 201 average time/residue: 0.4820 time to fit residues: 108.1527 Evaluate side-chains 206 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062415 restraints weight = 33901.386| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.81 r_work: 0.2723 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14465 Z= 0.122 Angle : 0.660 9.281 19675 Z= 0.327 Chirality : 0.045 0.216 2260 Planarity : 0.004 0.078 2435 Dihedral : 5.354 24.106 2195 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.98 % Allowed : 16.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.20), residues: 1710 helix: -0.11 (0.21), residues: 600 sheet: 0.47 (0.29), residues: 345 loop : -1.22 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 75 TYR 0.015 0.001 TYR B 317 PHE 0.012 0.001 PHE E 258 TRP 0.060 0.001 TRP C 255 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00277 (14440) covalent geometry : angle 0.65485 (19610) SS BOND : bond 0.00375 ( 10) SS BOND : angle 2.15326 ( 20) hydrogen bonds : bond 0.03377 ( 575) hydrogen bonds : angle 4.01099 ( 2070) link_BETA1-4 : bond 0.00314 ( 10) link_BETA1-4 : angle 1.55582 ( 30) link_NAG-ASN : bond 0.00025 ( 5) link_NAG-ASN : angle 0.62081 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9280 (mmm) cc_final: 0.8919 (mmt) REVERT: A 156 MET cc_start: 0.9237 (mtp) cc_final: 0.8967 (mmm) REVERT: A 202 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8767 (mm110) REVERT: A 243 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8424 (mpp) REVERT: A 300 ASP cc_start: 0.9303 (m-30) cc_final: 0.8973 (m-30) REVERT: A 306 CYS cc_start: 0.8534 (m) cc_final: 0.8275 (t) REVERT: B 71 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9226 (p) REVERT: B 72 MET cc_start: 0.9182 (mtm) cc_final: 0.8968 (mmm) REVERT: B 156 MET cc_start: 0.9333 (mmt) cc_final: 0.8872 (mmt) REVERT: B 173 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8038 (mm-30) REVERT: B 202 GLN cc_start: 0.9177 (mt0) cc_final: 0.8975 (mt0) REVERT: B 241 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8765 (mp) REVERT: B 243 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8351 (mpp) REVERT: B 300 ASP cc_start: 0.9343 (m-30) cc_final: 0.8950 (m-30) REVERT: B 306 CYS cc_start: 0.8545 (m) cc_final: 0.8287 (t) REVERT: B 317 TYR cc_start: 0.8398 (t80) cc_final: 0.8114 (t80) REVERT: C 43 ARG cc_start: 0.9400 (mtm-85) cc_final: 0.9158 (mtm-85) REVERT: C 156 MET cc_start: 0.9197 (tpp) cc_final: 0.8602 (tpp) REVERT: C 163 MET cc_start: 0.8561 (mpp) cc_final: 0.8074 (mtp) REVERT: C 202 GLN cc_start: 0.9154 (mt0) cc_final: 0.8244 (mp10) REVERT: C 242 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: C 243 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: C 300 ASP cc_start: 0.9292 (m-30) cc_final: 0.8952 (m-30) REVERT: D 31 ASP cc_start: 0.9047 (m-30) cc_final: 0.8459 (m-30) REVERT: D 72 MET cc_start: 0.9209 (mtm) cc_final: 0.8930 (mmm) REVERT: D 75 ARG cc_start: 0.9105 (ttm110) cc_final: 0.8831 (mtp-110) REVERT: D 107 ASP cc_start: 0.9318 (t0) cc_final: 0.8990 (OUTLIER) REVERT: D 156 MET cc_start: 0.9047 (mmm) cc_final: 0.8690 (tpp) REVERT: D 173 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7954 (mm-30) REVERT: D 202 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8820 (mm-40) REVERT: D 241 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8761 (mp) REVERT: D 242 GLN cc_start: 0.8808 (tp40) cc_final: 0.8459 (tm-30) REVERT: D 243 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8519 (mpp) REVERT: D 292 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.8998 (mtmm) REVERT: D 300 ASP cc_start: 0.9271 (m-30) cc_final: 0.8872 (m-30) REVERT: D 391 MET cc_start: 0.0529 (tpt) cc_final: 0.0283 (tpp) REVERT: D 420 PHE cc_start: 0.8719 (m-80) cc_final: 0.8499 (m-80) REVERT: E 24 MET cc_start: 0.8576 (ptm) cc_final: 0.8296 (tmt) REVERT: E 72 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8985 (mmt) REVERT: E 156 MET cc_start: 0.9524 (tpp) cc_final: 0.9172 (mmt) REVERT: E 202 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8889 (mm-40) REVERT: E 243 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: E 292 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9125 (mtmm) REVERT: E 300 ASP cc_start: 0.9311 (m-30) cc_final: 0.9024 (m-30) REVERT: E 306 CYS cc_start: 0.8568 (m) cc_final: 0.8295 (t) outliers start: 45 outliers final: 21 residues processed: 203 average time/residue: 0.4740 time to fit residues: 107.4264 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061176 restraints weight = 34168.343| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.81 r_work: 0.2692 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14465 Z= 0.190 Angle : 0.683 8.355 19675 Z= 0.344 Chirality : 0.046 0.217 2260 Planarity : 0.004 0.084 2435 Dihedral : 5.398 26.136 2195 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.91 % Allowed : 17.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1710 helix: -0.05 (0.21), residues: 605 sheet: 0.59 (0.30), residues: 345 loop : -1.27 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 75 TYR 0.026 0.002 TYR E 317 PHE 0.013 0.001 PHE A 203 TRP 0.044 0.001 TRP C 255 HIS 0.001 0.000 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00437 (14440) covalent geometry : angle 0.67497 (19610) SS BOND : bond 0.00512 ( 10) SS BOND : angle 2.68738 ( 20) hydrogen bonds : bond 0.03460 ( 575) hydrogen bonds : angle 4.11329 ( 2070) link_BETA1-4 : bond 0.00370 ( 10) link_BETA1-4 : angle 1.60635 ( 30) link_NAG-ASN : bond 0.00220 ( 5) link_NAG-ASN : angle 0.89891 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9283 (mmm) cc_final: 0.8904 (mmt) REVERT: A 156 MET cc_start: 0.9267 (mtp) cc_final: 0.8686 (mmm) REVERT: A 166 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7276 (mm-40) REVERT: A 202 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8783 (mm110) REVERT: A 243 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8436 (mpp) REVERT: A 300 ASP cc_start: 0.9316 (m-30) cc_final: 0.8985 (m-30) REVERT: A 306 CYS cc_start: 0.8570 (m) cc_final: 0.8318 (t) REVERT: A 317 TYR cc_start: 0.8473 (t80) cc_final: 0.8270 (t80) REVERT: B 71 THR cc_start: 0.9495 (OUTLIER) cc_final: 0.9201 (p) REVERT: B 72 MET cc_start: 0.9198 (mtm) cc_final: 0.8958 (mmm) REVERT: B 156 MET cc_start: 0.9353 (mmt) cc_final: 0.8891 (mmt) REVERT: B 173 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8027 (mm-30) REVERT: B 241 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 243 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: B 300 ASP cc_start: 0.9346 (m-30) cc_final: 0.8949 (m-30) REVERT: B 306 CYS cc_start: 0.8563 (m) cc_final: 0.8290 (t) REVERT: B 317 TYR cc_start: 0.8418 (t80) cc_final: 0.8114 (t80) REVERT: C 156 MET cc_start: 0.9003 (tpp) cc_final: 0.8769 (mmt) REVERT: C 163 MET cc_start: 0.8599 (mpp) cc_final: 0.8162 (mtp) REVERT: C 166 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6424 (mt0) REVERT: C 243 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8454 (mmm) REVERT: C 300 ASP cc_start: 0.9299 (m-30) cc_final: 0.8958 (m-30) REVERT: C 317 TYR cc_start: 0.8448 (t80) cc_final: 0.8223 (t80) REVERT: D 31 ASP cc_start: 0.9039 (m-30) cc_final: 0.8486 (m-30) REVERT: D 72 MET cc_start: 0.9208 (mtm) cc_final: 0.8920 (mmm) REVERT: D 75 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8828 (mtp-110) REVERT: D 107 ASP cc_start: 0.9355 (t0) cc_final: 0.9022 (p0) REVERT: D 156 MET cc_start: 0.9068 (mmm) cc_final: 0.8724 (tpp) REVERT: D 173 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7917 (mm-30) REVERT: D 202 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8740 (mp10) REVERT: D 241 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8755 (mp) REVERT: D 242 GLN cc_start: 0.8785 (tp40) cc_final: 0.8448 (tm-30) REVERT: D 243 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8477 (mpp) REVERT: D 300 ASP cc_start: 0.9253 (m-30) cc_final: 0.8848 (m-30) REVERT: D 391 MET cc_start: 0.0512 (tpt) cc_final: 0.0287 (tpp) REVERT: D 420 PHE cc_start: 0.8719 (m-80) cc_final: 0.8500 (m-80) REVERT: E 24 MET cc_start: 0.8347 (ptm) cc_final: 0.8053 (tmt) REVERT: E 72 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8950 (mmt) REVERT: E 156 MET cc_start: 0.9502 (tpp) cc_final: 0.9161 (mmt) REVERT: E 202 GLN cc_start: 0.9201 (mt0) cc_final: 0.8943 (mm-40) REVERT: E 243 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8697 (mmm) REVERT: E 300 ASP cc_start: 0.9292 (m-30) cc_final: 0.8994 (m-30) REVERT: E 306 CYS cc_start: 0.8553 (m) cc_final: 0.8317 (t) outliers start: 44 outliers final: 24 residues processed: 192 average time/residue: 0.5071 time to fit residues: 108.6674 Evaluate side-chains 203 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 0.0370 chunk 124 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 202 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062960 restraints weight = 33639.157| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.83 r_work: 0.2736 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14465 Z= 0.121 Angle : 0.691 11.579 19675 Z= 0.340 Chirality : 0.045 0.214 2260 Planarity : 0.004 0.086 2435 Dihedral : 5.350 24.369 2195 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.52 % Allowed : 17.81 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1710 helix: 0.02 (0.21), residues: 600 sheet: 0.60 (0.29), residues: 345 loop : -1.27 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 75 TYR 0.028 0.001 TYR E 317 PHE 0.014 0.001 PHE A 203 TRP 0.038 0.001 TRP C 255 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00276 (14440) covalent geometry : angle 0.68586 (19610) SS BOND : bond 0.00383 ( 10) SS BOND : angle 2.31184 ( 20) hydrogen bonds : bond 0.03417 ( 575) hydrogen bonds : angle 4.00430 ( 2070) link_BETA1-4 : bond 0.00301 ( 10) link_BETA1-4 : angle 1.47661 ( 30) link_NAG-ASN : bond 0.00071 ( 5) link_NAG-ASN : angle 0.56466 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.540 Fit side-chains REVERT: A 105 MET cc_start: 0.9278 (mmm) cc_final: 0.8985 (mmt) REVERT: A 156 MET cc_start: 0.9186 (mtp) cc_final: 0.8272 (tpp) REVERT: A 166 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7202 (mt0) REVERT: A 202 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8771 (mm110) REVERT: A 242 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 243 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8576 (mmm) REVERT: A 300 ASP cc_start: 0.9303 (m-30) cc_final: 0.8960 (m-30) REVERT: A 306 CYS cc_start: 0.8528 (m) cc_final: 0.8277 (t) REVERT: A 317 TYR cc_start: 0.8403 (t80) cc_final: 0.8161 (t80) REVERT: B 43 ARG cc_start: 0.9424 (mtm-85) cc_final: 0.9222 (mtm180) REVERT: B 72 MET cc_start: 0.9192 (mtm) cc_final: 0.8986 (mmm) REVERT: B 105 MET cc_start: 0.9286 (mmm) cc_final: 0.8620 (mpm) REVERT: B 156 MET cc_start: 0.9330 (mmt) cc_final: 0.8868 (mmt) REVERT: B 173 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7986 (mm-30) REVERT: B 241 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 243 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8218 (mpp) REVERT: B 300 ASP cc_start: 0.9343 (m-30) cc_final: 0.8966 (m-30) REVERT: B 306 CYS cc_start: 0.8496 (m) cc_final: 0.8271 (t) REVERT: B 317 TYR cc_start: 0.8401 (t80) cc_final: 0.8119 (t80) REVERT: C 43 ARG cc_start: 0.9449 (mtm-85) cc_final: 0.9239 (mtm180) REVERT: C 163 MET cc_start: 0.8526 (mpp) cc_final: 0.8023 (mtp) REVERT: C 166 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7089 (tp40) REVERT: C 202 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: C 243 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: C 300 ASP cc_start: 0.9287 (m-30) cc_final: 0.8950 (m-30) REVERT: C 317 TYR cc_start: 0.8463 (t80) cc_final: 0.8208 (t80) REVERT: D 72 MET cc_start: 0.9202 (mtm) cc_final: 0.8960 (mmm) REVERT: D 75 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8843 (mtp-110) REVERT: D 107 ASP cc_start: 0.9354 (t0) cc_final: 0.9013 (p0) REVERT: D 173 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7932 (mm-30) REVERT: D 202 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8736 (mm110) REVERT: D 241 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8751 (mp) REVERT: D 242 GLN cc_start: 0.8693 (tp40) cc_final: 0.8368 (tm-30) REVERT: D 243 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8477 (mpp) REVERT: D 292 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.8931 (mtmm) REVERT: D 300 ASP cc_start: 0.9231 (m-30) cc_final: 0.8819 (m-30) REVERT: D 317 TYR cc_start: 0.8511 (t80) cc_final: 0.8240 (t80) REVERT: D 391 MET cc_start: 0.0457 (tpt) cc_final: 0.0235 (tpp) REVERT: D 420 PHE cc_start: 0.8684 (m-80) cc_final: 0.8471 (m-80) REVERT: E 24 MET cc_start: 0.8221 (ptm) cc_final: 0.7944 (tmt) REVERT: E 72 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8969 (mmt) REVERT: E 156 MET cc_start: 0.9504 (tpp) cc_final: 0.9151 (mmt) REVERT: E 202 GLN cc_start: 0.9139 (mt0) cc_final: 0.8882 (mm-40) REVERT: E 243 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8672 (mmm) outliers start: 38 outliers final: 17 residues processed: 194 average time/residue: 0.5092 time to fit residues: 109.5442 Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 168 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 167 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 166 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062640 restraints weight = 33764.995| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.82 r_work: 0.2727 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14465 Z= 0.137 Angle : 0.680 11.228 19675 Z= 0.339 Chirality : 0.045 0.208 2260 Planarity : 0.004 0.085 2435 Dihedral : 5.275 24.735 2195 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.25 % Allowed : 18.15 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1710 helix: 0.14 (0.21), residues: 600 sheet: 0.67 (0.29), residues: 345 loop : -1.30 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 75 TYR 0.023 0.001 TYR D 317 PHE 0.016 0.001 PHE A 203 TRP 0.034 0.001 TRP C 255 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00318 (14440) covalent geometry : angle 0.67418 (19610) SS BOND : bond 0.00402 ( 10) SS BOND : angle 2.44648 ( 20) hydrogen bonds : bond 0.03448 ( 575) hydrogen bonds : angle 3.98657 ( 2070) link_BETA1-4 : bond 0.00315 ( 10) link_BETA1-4 : angle 1.46709 ( 30) link_NAG-ASN : bond 0.00064 ( 5) link_NAG-ASN : angle 0.69019 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.84 seconds wall clock time: 78 minutes 38.20 seconds (4718.20 seconds total)