Starting phenix.real_space_refine on Wed Mar 4 14:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm6_20389/03_2026/6pm6_20389.map" } resolution = 2.9 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= 0.060 sd= 3.254 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 100 5.16 5 C 9185 2.51 5 N 2260 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 14100 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 3.37, per 1000 atoms: 0.24 Number of scatterers: 14100 At special positions: 0 Unit cell: (106.167, 102.875, 134.972, 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 100 16.00 O 2555 8.00 N 2260 7.00 C 9185 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=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 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=2.03 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=2.03 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=2.03 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 D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 635.5 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: 65 helices and 25 sheets defined 38.6% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.523A pdb=" N PHE A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.972A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.522A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.951A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.518A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 286 removed outlier: 3.575A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.550A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.577A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 4.010A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.541A pdb=" N PHE D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.014A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.556A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.024A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.800A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.550A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 286 removed outlier: 3.558A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 283 " --> pdb=" O MET D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 304 through 325 removed outlier: 3.551A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 406 removed outlier: 4.396A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 427 removed outlier: 4.009A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.544A pdb=" N PHE B 29 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.904A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.056A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.530A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 286 removed outlier: 3.544A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 304 through 325 removed outlier: 3.637A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.552A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 427 removed outlier: 4.020A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.577A pdb=" N PHE C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.980A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.503A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.537A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 286 removed outlier: 3.538A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 304 through 325 removed outlier: 3.575A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.561A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 427 removed outlier: 3.942A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.567A pdb=" N PHE E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.964A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.531A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.980A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.538A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 286 removed outlier: 4.224A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 283 " --> pdb=" O MET E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 304 through 325 removed outlier: 3.567A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 406 removed outlier: 3.554A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 427 removed outlier: 3.964A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.556A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.485A 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: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.277A 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 'D' and resid 98 through 100 removed outlier: 3.630A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.555A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.582A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.587A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.545A 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 124 removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.246A 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 217 677 hydrogen bonds defined for protein. 1968 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: 2.43 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4313 1.34 - 1.47: 3630 1.47 - 1.59: 6332 1.59 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14445 Sorted by residual: bond pdb=" C PHE D 410 " pdb=" N PRO D 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C PHE A 410 " pdb=" N PRO A 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.70e+01 bond pdb=" C PHE E 410 " pdb=" N PRO E 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.69e+01 bond pdb=" C PHE C 410 " pdb=" N PRO C 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C PHE B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.61e+01 ... (remaining 14440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 18878 2.07 - 4.14: 582 4.14 - 6.21: 96 6.21 - 8.28: 45 8.28 - 10.35: 9 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8347 16.01 - 32.02: 339 32.02 - 48.03: 51 48.03 - 64.05: 45 64.05 - 80.06: 33 Dihedral angle restraints: 8815 sinusoidal: 3700 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+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 51.08 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 51.12 41.88 1 1.00e+01 1.00e-02 2.45e+01 ... (remaining 8812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1553 0.051 - 0.101: 538 0.101 - 0.152: 139 0.152 - 0.202: 15 0.202 - 0.253: 15 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.03e+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 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 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 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO B 411 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.16e+00 pdb=" N PRO D 411 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO A 411 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.042 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4537 2.85 - 3.36: 12059 3.36 - 3.87: 22417 3.87 - 4.39: 26556 4.39 - 4.90: 44747 Nonbonded interactions: 110316 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.336 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.344 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.346 3.040 ... (remaining 110311 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 'D' selection = chain 'B' selection = chain 'C' 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: 0.010 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.110 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.005 0.046 14470 Z= 0.227 Angle : 0.929 10.349 19675 Z= 0.483 Chirality : 0.055 0.253 2260 Planarity : 0.007 0.076 2430 Dihedral : 11.654 80.057 5465 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -4.86 (0.15), residues: 1710 helix: -4.79 (0.07), residues: 550 sheet: -1.89 (0.23), residues: 385 loop : -2.57 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 147 TYR 0.017 0.002 TYR D 425 PHE 0.021 0.002 PHE A 115 TRP 0.019 0.002 TRP A 110 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00470 (14445) covalent geometry : angle 0.92210 (19610) SS BOND : bond 0.00558 ( 10) SS BOND : angle 2.83241 ( 20) hydrogen bonds : bond 0.28789 ( 532) hydrogen bonds : angle 9.72342 ( 1968) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 1.85193 ( 30) link_NAG-ASN : bond 0.00105 ( 5) link_NAG-ASN : angle 1.66344 ( 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 403 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.511 Fit side-chains REVERT: A 75 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6919 (ttm110) REVERT: A 206 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8047 (mttt) REVERT: A 210 ASP cc_start: 0.8048 (m-30) cc_final: 0.7306 (t0) REVERT: A 222 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7579 (pttt) REVERT: A 292 LYS cc_start: 0.8062 (mttt) cc_final: 0.7690 (mttp) REVERT: A 391 MET cc_start: 0.6841 (mtp) cc_final: 0.6363 (tmm) REVERT: A 419 ILE cc_start: 0.8385 (mt) cc_final: 0.8131 (mp) REVERT: D 32 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7965 (tmtt) REVERT: D 75 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7024 (ttm110) REVERT: D 206 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8012 (mtmm) REVERT: D 210 ASP cc_start: 0.7951 (m-30) cc_final: 0.7046 (t0) REVERT: D 222 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7490 (pttt) REVERT: D 292 LYS cc_start: 0.8120 (mttt) cc_final: 0.7861 (mttp) REVERT: D 391 MET cc_start: 0.6743 (mtp) cc_final: 0.5594 (tpt) REVERT: D 420 PHE cc_start: 0.7334 (t80) cc_final: 0.7096 (t80) REVERT: B 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8034 (tmtt) REVERT: B 210 ASP cc_start: 0.7886 (m-30) cc_final: 0.7079 (t0) REVERT: B 222 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7573 (pttt) REVERT: B 279 MET cc_start: 0.8169 (mmm) cc_final: 0.7597 (mmt) REVERT: B 292 LYS cc_start: 0.8105 (mttt) cc_final: 0.7756 (mttp) REVERT: B 401 ARG cc_start: 0.5233 (tpt170) cc_final: 0.4987 (tmt90) REVERT: C 28 GLU cc_start: 0.7625 (tp30) cc_final: 0.7023 (tp30) REVERT: C 32 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8095 (tttp) REVERT: C 75 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7149 (mtp-110) REVERT: C 206 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7896 (mtmm) REVERT: C 210 ASP cc_start: 0.7846 (m-30) cc_final: 0.7070 (t0) REVERT: C 222 LYS cc_start: 0.7777 (ptmm) cc_final: 0.7488 (pttt) REVERT: C 420 PHE cc_start: 0.7290 (t80) cc_final: 0.7039 (t80) REVERT: E 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8044 (tmtt) REVERT: E 75 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7128 (ttm110) REVERT: E 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8100 (mtmm) REVERT: E 210 ASP cc_start: 0.7856 (m-30) cc_final: 0.7050 (t0) REVERT: E 391 MET cc_start: 0.6643 (mtp) cc_final: 0.6382 (ttp) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.5164 time to fit residues: 230.4127 Evaluate side-chains 285 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 77 ASN D 219 ASN D 231 HIS B 77 ASN B 231 HIS C 77 ASN C 219 ASN E 77 ASN E 219 ASN E 231 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125023 restraints weight = 15620.498| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.12 r_work: 0.3212 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14470 Z= 0.149 Angle : 0.792 14.839 19675 Z= 0.401 Chirality : 0.049 0.318 2260 Planarity : 0.005 0.052 2430 Dihedral : 10.296 59.848 2185 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.64 % Allowed : 11.09 % Favored : 86.27 % 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: -3.59 (0.17), residues: 1710 helix: -3.09 (0.15), residues: 565 sheet: -1.05 (0.26), residues: 385 loop : -2.41 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 75 TYR 0.017 0.002 TYR B 317 PHE 0.014 0.001 PHE D 309 TRP 0.010 0.002 TRP B 84 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00321 (14445) covalent geometry : angle 0.76922 (19610) SS BOND : bond 0.01257 ( 10) SS BOND : angle 5.07616 ( 20) hydrogen bonds : bond 0.05675 ( 532) hydrogen bonds : angle 5.99151 ( 1968) link_BETA1-4 : bond 0.00244 ( 10) link_BETA1-4 : angle 2.69753 ( 30) link_NAG-ASN : bond 0.00174 ( 5) link_NAG-ASN : angle 0.57089 ( 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 352 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6580 (ttm110) REVERT: A 96 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7159 (t0) REVERT: A 97 ASP cc_start: 0.7438 (m-30) cc_final: 0.6945 (t0) REVERT: A 206 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7579 (mttt) REVERT: A 212 ARG cc_start: 0.7515 (ptp-110) cc_final: 0.7202 (ptp-110) REVERT: A 262 MET cc_start: 0.3587 (mpp) cc_final: 0.3348 (mpp) REVERT: A 292 LYS cc_start: 0.7397 (mttt) cc_final: 0.7107 (mttp) REVERT: A 391 MET cc_start: 0.6817 (mtp) cc_final: 0.6372 (tmm) REVERT: A 420 PHE cc_start: 0.7692 (t80) cc_final: 0.6929 (t80) REVERT: D 75 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6665 (ttm110) REVERT: D 206 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7581 (mtmm) REVERT: D 243 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.5959 (mpt) REVERT: D 292 LYS cc_start: 0.7414 (mttt) cc_final: 0.7187 (mttp) REVERT: D 391 MET cc_start: 0.6825 (mtp) cc_final: 0.6394 (ttp) REVERT: B 222 LYS cc_start: 0.7081 (ptmm) cc_final: 0.6656 (pttt) REVERT: B 243 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.5587 (mpt) REVERT: B 292 LYS cc_start: 0.7335 (mttt) cc_final: 0.7072 (mttp) REVERT: B 401 ARG cc_start: 0.4696 (tpt170) cc_final: 0.4459 (tpt-90) REVERT: B 420 PHE cc_start: 0.7784 (t80) cc_final: 0.7298 (t80) REVERT: C 75 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.6768 (mtp-110) REVERT: C 96 ASP cc_start: 0.7873 (t0) cc_final: 0.7556 (t0) REVERT: C 97 ASP cc_start: 0.7331 (m-30) cc_final: 0.6651 (t0) REVERT: C 105 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7160 (mmp) REVERT: C 206 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7347 (mtmm) REVERT: C 243 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.5701 (mpt) REVERT: C 401 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.4998 (tmt90) REVERT: C 420 PHE cc_start: 0.7364 (t80) cc_final: 0.7086 (t80) REVERT: E 75 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6848 (ttm110) REVERT: E 96 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7114 (t0) REVERT: E 97 ASP cc_start: 0.7696 (m-30) cc_final: 0.7101 (t0) REVERT: E 206 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7588 (mmmm) REVERT: E 210 ASP cc_start: 0.7869 (m-30) cc_final: 0.6925 (t0) REVERT: E 243 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5730 (mpt) REVERT: E 262 MET cc_start: 0.3941 (mpp) cc_final: 0.3446 (mpp) REVERT: E 391 MET cc_start: 0.6908 (mtp) cc_final: 0.6443 (ttp) outliers start: 40 outliers final: 13 residues processed: 337 average time/residue: 0.5193 time to fit residues: 193.7578 Evaluate side-chains 289 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN D 219 ASN B 77 ASN B 82 GLN B 219 ASN C 77 ASN C 82 GLN C 219 ASN C 231 HIS E 82 GLN E 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111974 restraints weight = 15759.169| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.16 r_work: 0.2943 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 14470 Z= 0.340 Angle : 0.918 14.091 19675 Z= 0.465 Chirality : 0.054 0.299 2260 Planarity : 0.006 0.044 2430 Dihedral : 8.818 56.723 2185 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.07 % Allowed : 13.47 % Favored : 80.46 % 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: -2.76 (0.19), residues: 1710 helix: -2.33 (0.19), residues: 565 sheet: -0.37 (0.28), residues: 370 loop : -2.10 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 135 TYR 0.019 0.003 TYR A 144 PHE 0.022 0.003 PHE B 124 TRP 0.025 0.003 TRP E 255 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00809 (14445) covalent geometry : angle 0.89719 (19610) SS BOND : bond 0.00979 ( 10) SS BOND : angle 5.25480 ( 20) hydrogen bonds : bond 0.05202 ( 532) hydrogen bonds : angle 5.44265 ( 1968) link_BETA1-4 : bond 0.00560 ( 10) link_BETA1-4 : angle 2.87388 ( 30) link_NAG-ASN : bond 0.00141 ( 5) link_NAG-ASN : angle 0.64357 ( 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 390 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 298 time to evaluate : 0.525 Fit side-chains REVERT: A 49 LYS cc_start: 0.8564 (mttt) cc_final: 0.8174 (mtpt) REVERT: A 75 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6715 (ttm110) REVERT: A 97 ASP cc_start: 0.7686 (m-30) cc_final: 0.6969 (t0) REVERT: A 100 ASP cc_start: 0.7354 (p0) cc_final: 0.7140 (t70) REVERT: A 188 GLU cc_start: 0.8561 (mp0) cc_final: 0.8357 (mp0) REVERT: A 292 LYS cc_start: 0.7691 (mttt) cc_final: 0.7379 (mttp) REVERT: A 391 MET cc_start: 0.7024 (mtp) cc_final: 0.6676 (tmm) REVERT: A 420 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6956 (t80) REVERT: D 75 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6787 (ttm110) REVERT: D 97 ASP cc_start: 0.7676 (m-30) cc_final: 0.7035 (t0) REVERT: D 188 GLU cc_start: 0.8580 (mp0) cc_final: 0.8350 (mp0) REVERT: D 206 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7585 (mtmm) REVERT: D 207 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7475 (tp30) REVERT: D 210 ASP cc_start: 0.7690 (m-30) cc_final: 0.7309 (m-30) REVERT: D 227 GLU cc_start: 0.8158 (pt0) cc_final: 0.7893 (pt0) REVERT: D 229 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6859 (mmt90) REVERT: D 292 LYS cc_start: 0.7852 (mttt) cc_final: 0.7627 (mttm) REVERT: D 391 MET cc_start: 0.6893 (mtp) cc_final: 0.6515 (ttp) REVERT: B 28 GLU cc_start: 0.7648 (tp30) cc_final: 0.6967 (tp30) REVERT: B 96 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7506 (t0) REVERT: B 97 ASP cc_start: 0.7721 (m-30) cc_final: 0.7060 (t0) REVERT: B 126 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6807 (pm20) REVERT: B 181 ASP cc_start: 0.7915 (m-30) cc_final: 0.7457 (m-30) REVERT: B 207 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7410 (tp30) REVERT: B 243 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.5571 (mpt) REVERT: B 420 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7263 (t80) REVERT: C 28 GLU cc_start: 0.7470 (tp30) cc_final: 0.6905 (tp30) REVERT: C 75 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6609 (ttm110) REVERT: C 96 ASP cc_start: 0.7955 (t0) cc_final: 0.7597 (t0) REVERT: C 97 ASP cc_start: 0.7579 (m-30) cc_final: 0.6796 (t0) REVERT: C 188 GLU cc_start: 0.8638 (mp0) cc_final: 0.8363 (mp0) REVERT: C 227 GLU cc_start: 0.8343 (pt0) cc_final: 0.8082 (pt0) REVERT: C 243 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5816 (mpt) REVERT: C 401 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.5088 (tmt90) REVERT: C 418 ASN cc_start: 0.7018 (m-40) cc_final: 0.6719 (m110) REVERT: C 420 PHE cc_start: 0.7412 (t80) cc_final: 0.7101 (t80) REVERT: E 75 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.6658 (ttm110) REVERT: E 96 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7430 (t0) REVERT: E 97 ASP cc_start: 0.7879 (m-30) cc_final: 0.7201 (t0) REVERT: E 206 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7636 (mtmm) REVERT: E 207 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7521 (tp30) REVERT: E 227 GLU cc_start: 0.8174 (pt0) cc_final: 0.7810 (pt0) REVERT: E 243 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.5795 (mpt) REVERT: E 262 MET cc_start: 0.3747 (mpp) cc_final: 0.3438 (mpp) REVERT: E 391 MET cc_start: 0.6828 (mtp) cc_final: 0.6491 (tmm) outliers start: 92 outliers final: 33 residues processed: 345 average time/residue: 0.5162 time to fit residues: 197.3512 Evaluate side-chains 320 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 162 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 282 GLN D 85 ASN D 141 ASN D 219 ASN B 77 ASN B 219 ASN C 77 ASN C 141 ASN C 219 ASN E 58 ASN E 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117906 restraints weight = 15452.760| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.16 r_work: 0.3032 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14470 Z= 0.132 Angle : 0.712 10.281 19675 Z= 0.356 Chirality : 0.046 0.206 2260 Planarity : 0.004 0.038 2430 Dihedral : 7.046 59.428 2185 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.29 % Allowed : 18.28 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.25 (0.19), residues: 1710 helix: -1.79 (0.20), residues: 555 sheet: 0.28 (0.30), residues: 320 loop : -1.99 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.013 0.002 TYR C 317 PHE 0.011 0.001 PHE A 115 TRP 0.026 0.002 TRP E 255 HIS 0.001 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00296 (14445) covalent geometry : angle 0.69303 (19610) SS BOND : bond 0.00344 ( 10) SS BOND : angle 4.29325 ( 20) hydrogen bonds : bond 0.03996 ( 532) hydrogen bonds : angle 4.88295 ( 1968) link_BETA1-4 : bond 0.00356 ( 10) link_BETA1-4 : angle 2.46552 ( 30) link_NAG-ASN : bond 0.00129 ( 5) link_NAG-ASN : angle 0.41658 ( 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 369 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.546 Fit side-chains REVERT: A 75 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6780 (ttm110) REVERT: A 97 ASP cc_start: 0.7596 (m-30) cc_final: 0.6907 (t0) REVERT: A 101 LEU cc_start: 0.7344 (mt) cc_final: 0.7088 (mp) REVERT: A 243 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5801 (mpt) REVERT: A 260 ILE cc_start: 0.4613 (OUTLIER) cc_final: 0.4397 (pt) REVERT: A 292 LYS cc_start: 0.7611 (mttt) cc_final: 0.7298 (mttp) REVERT: A 391 MET cc_start: 0.6884 (mtp) cc_final: 0.6547 (tmm) REVERT: A 420 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6954 (t80) REVERT: D 75 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.6981 (ttm110) REVERT: D 97 ASP cc_start: 0.7589 (m-30) cc_final: 0.6967 (t0) REVERT: D 206 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7624 (mtmm) REVERT: D 207 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7429 (tp30) REVERT: D 210 ASP cc_start: 0.7626 (m-30) cc_final: 0.7263 (m-30) REVERT: D 227 GLU cc_start: 0.8093 (pt0) cc_final: 0.7787 (pt0) REVERT: D 229 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6809 (mmt90) REVERT: D 243 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5759 (mpt) REVERT: D 292 LYS cc_start: 0.7704 (mttt) cc_final: 0.7500 (mttm) REVERT: D 391 MET cc_start: 0.6799 (mtp) cc_final: 0.6435 (ttp) REVERT: D 420 PHE cc_start: 0.7244 (t80) cc_final: 0.6972 (t80) REVERT: B 28 GLU cc_start: 0.7590 (tp30) cc_final: 0.6887 (tp30) REVERT: B 96 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 97 ASP cc_start: 0.7637 (m-30) cc_final: 0.7000 (t0) REVERT: B 126 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6651 (pm20) REVERT: B 181 ASP cc_start: 0.7935 (m-30) cc_final: 0.7537 (m-30) REVERT: B 188 GLU cc_start: 0.8648 (mp0) cc_final: 0.8419 (mp0) REVERT: B 207 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7406 (tp30) REVERT: B 227 GLU cc_start: 0.8080 (pt0) cc_final: 0.7646 (pt0) REVERT: C 28 GLU cc_start: 0.7464 (tp30) cc_final: 0.6856 (tp30) REVERT: C 75 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.6863 (ttm110) REVERT: C 97 ASP cc_start: 0.7506 (m-30) cc_final: 0.6717 (t0) REVERT: C 156 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6611 (mmt) REVERT: C 163 MET cc_start: 0.7820 (mtm) cc_final: 0.7560 (mpp) REVERT: C 188 GLU cc_start: 0.8588 (mp0) cc_final: 0.8377 (mp0) REVERT: C 227 GLU cc_start: 0.8186 (pt0) cc_final: 0.7798 (pt0) REVERT: C 243 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5593 (mpt) REVERT: C 401 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.5116 (tmt90) REVERT: E 75 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.6942 (ttm110) REVERT: E 97 ASP cc_start: 0.7751 (m-30) cc_final: 0.7102 (t0) REVERT: E 206 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7646 (mtmm) REVERT: E 207 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7548 (tp30) REVERT: E 229 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7144 (mmt90) REVERT: E 262 MET cc_start: 0.3899 (mpp) cc_final: 0.3510 (mpp) REVERT: E 268 ARG cc_start: 0.6625 (mtm180) cc_final: 0.6404 (mtp180) REVERT: E 391 MET cc_start: 0.6820 (mtp) cc_final: 0.6473 (ttp) REVERT: E 418 ASN cc_start: 0.6760 (m-40) cc_final: 0.6474 (m110) REVERT: E 420 PHE cc_start: 0.7341 (t80) cc_final: 0.7138 (t80) outliers start: 65 outliers final: 16 residues processed: 325 average time/residue: 0.5363 time to fit residues: 192.8702 Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 99 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 219 ASN A 231 HIS D 77 ASN D 219 ASN D 282 GLN B 77 ASN B 219 ASN C 77 ASN C 219 ASN E 62 ASN E 77 ASN E 219 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118065 restraints weight = 15315.953| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.24 r_work: 0.3184 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14470 Z= 0.127 Angle : 0.671 8.508 19675 Z= 0.338 Chirality : 0.045 0.158 2260 Planarity : 0.004 0.037 2430 Dihedral : 5.889 53.664 2185 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.36 % Allowed : 18.48 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.92 (0.19), residues: 1710 helix: -1.39 (0.21), residues: 575 sheet: 0.36 (0.30), residues: 320 loop : -1.83 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 229 TYR 0.012 0.001 TYR E 317 PHE 0.012 0.001 PHE B 258 TRP 0.029 0.001 TRP E 255 HIS 0.001 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00292 (14445) covalent geometry : angle 0.65787 (19610) SS BOND : bond 0.00303 ( 10) SS BOND : angle 3.60947 ( 20) hydrogen bonds : bond 0.03845 ( 532) hydrogen bonds : angle 4.59249 ( 1968) link_BETA1-4 : bond 0.00450 ( 10) link_BETA1-4 : angle 2.01454 ( 30) link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 0.39773 ( 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 345 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.540 Fit side-chains REVERT: A 75 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7371 (ttm110) REVERT: A 97 ASP cc_start: 0.7802 (m-30) cc_final: 0.7202 (t0) REVERT: A 292 LYS cc_start: 0.7992 (mttt) cc_final: 0.7652 (mttp) REVERT: A 391 MET cc_start: 0.7005 (mtp) cc_final: 0.6700 (tmm) REVERT: A 420 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: D 75 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7449 (ttm110) REVERT: D 97 ASP cc_start: 0.7805 (m-30) cc_final: 0.7299 (t0) REVERT: D 207 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7612 (tp30) REVERT: D 210 ASP cc_start: 0.7983 (m-30) cc_final: 0.7695 (m-30) REVERT: D 212 ARG cc_start: 0.7369 (ptp-110) cc_final: 0.7164 (ptp-110) REVERT: D 227 GLU cc_start: 0.8438 (pt0) cc_final: 0.7948 (pt0) REVERT: D 229 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7439 (mmt90) REVERT: D 243 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6036 (mpt) REVERT: D 262 MET cc_start: 0.3960 (mpp) cc_final: 0.3727 (mpp) REVERT: D 292 LYS cc_start: 0.8067 (mttt) cc_final: 0.7862 (mttm) REVERT: D 391 MET cc_start: 0.6863 (mtp) cc_final: 0.6542 (ttp) REVERT: D 420 PHE cc_start: 0.7406 (t80) cc_final: 0.7186 (t80) REVERT: B 28 GLU cc_start: 0.7722 (tp30) cc_final: 0.6967 (tp30) REVERT: B 97 ASP cc_start: 0.7953 (m-30) cc_final: 0.7405 (t0) REVERT: B 126 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7037 (pm20) REVERT: B 207 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7594 (tp30) REVERT: B 243 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.5859 (mpt) REVERT: C 28 GLU cc_start: 0.7577 (tp30) cc_final: 0.6943 (tp30) REVERT: C 49 LYS cc_start: 0.8647 (mttt) cc_final: 0.8117 (mmtt) REVERT: C 75 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7262 (ttm110) REVERT: C 97 ASP cc_start: 0.7813 (m-30) cc_final: 0.7238 (t0) REVERT: C 229 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7402 (mmt90) REVERT: C 243 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.5720 (mpt) REVERT: E 75 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7326 (ttm110) REVERT: E 97 ASP cc_start: 0.8023 (m-30) cc_final: 0.7461 (t0) REVERT: E 130 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7809 (t0) REVERT: E 206 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7935 (mmmm) REVERT: E 207 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7707 (tp30) REVERT: E 229 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7580 (mmt90) REVERT: E 262 MET cc_start: 0.4323 (mpp) cc_final: 0.3868 (mpp) REVERT: E 391 MET cc_start: 0.6854 (mtp) cc_final: 0.6532 (ttp) REVERT: E 418 ASN cc_start: 0.7220 (m-40) cc_final: 0.6847 (m110) REVERT: E 420 PHE cc_start: 0.7525 (t80) cc_final: 0.7271 (t80) outliers start: 66 outliers final: 23 residues processed: 306 average time/residue: 0.5834 time to fit residues: 196.0952 Evaluate side-chains 298 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 219 ASN D 219 ASN D 282 GLN B 219 ASN C 219 ASN E 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117008 restraints weight = 15365.591| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.22 r_work: 0.3117 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 14470 Z= 0.274 Angle : 0.803 14.699 19675 Z= 0.403 Chirality : 0.049 0.188 2260 Planarity : 0.005 0.042 2430 Dihedral : 6.126 49.529 2185 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.74 % Allowed : 17.82 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -1.83 (0.20), residues: 1710 helix: -1.26 (0.22), residues: 575 sheet: 0.34 (0.30), residues: 325 loop : -1.81 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 135 TYR 0.015 0.002 TYR A 317 PHE 0.015 0.002 PHE C 115 TRP 0.030 0.002 TRP E 255 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00662 (14445) covalent geometry : angle 0.78150 (19610) SS BOND : bond 0.00662 ( 10) SS BOND : angle 5.33228 ( 20) hydrogen bonds : bond 0.04192 ( 532) hydrogen bonds : angle 4.76561 ( 1968) link_BETA1-4 : bond 0.00555 ( 10) link_BETA1-4 : angle 2.08168 ( 30) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 0.45371 ( 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 368 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 0.606 Fit side-chains REVERT: A 75 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7305 (ttm110) REVERT: A 97 ASP cc_start: 0.7913 (m-30) cc_final: 0.7378 (t0) REVERT: A 156 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7670 (mmt) REVERT: A 225 CYS cc_start: 0.7487 (t) cc_final: 0.7083 (t) REVERT: A 260 ILE cc_start: 0.5224 (OUTLIER) cc_final: 0.5008 (pt) REVERT: A 292 LYS cc_start: 0.8161 (mttt) cc_final: 0.7825 (mttp) REVERT: A 391 MET cc_start: 0.7032 (mtp) cc_final: 0.6701 (tmm) REVERT: A 420 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7092 (t80) REVERT: D 75 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7416 (ttm110) REVERT: D 97 ASP cc_start: 0.7905 (m-30) cc_final: 0.7357 (t0) REVERT: D 133 LEU cc_start: 0.8311 (tp) cc_final: 0.8100 (tt) REVERT: D 207 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7623 (tp30) REVERT: D 210 ASP cc_start: 0.7999 (m-30) cc_final: 0.7707 (m-30) REVERT: D 227 GLU cc_start: 0.8608 (pt0) cc_final: 0.8208 (pt0) REVERT: D 229 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7461 (mmt90) REVERT: D 243 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6149 (mpt) REVERT: D 292 LYS cc_start: 0.8214 (mttt) cc_final: 0.7917 (mttp) REVERT: D 391 MET cc_start: 0.6861 (mtp) cc_final: 0.6591 (tmm) REVERT: D 420 PHE cc_start: 0.7535 (t80) cc_final: 0.7234 (t80) REVERT: B 28 GLU cc_start: 0.7771 (tp30) cc_final: 0.7006 (tp30) REVERT: B 97 ASP cc_start: 0.8093 (m-30) cc_final: 0.7575 (t0) REVERT: B 126 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7064 (pm20) REVERT: B 207 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7622 (tp30) REVERT: B 229 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: B 243 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.5942 (mpt) REVERT: C 28 GLU cc_start: 0.7670 (tp30) cc_final: 0.7043 (tp30) REVERT: C 49 LYS cc_start: 0.8638 (mttt) cc_final: 0.8120 (mmtt) REVERT: C 75 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7247 (ttm110) REVERT: C 94 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6861 (t80) REVERT: C 97 ASP cc_start: 0.7899 (m-30) cc_final: 0.7289 (t0) REVERT: C 156 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.6707 (mmt) REVERT: C 229 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7560 (mmt90) REVERT: C 243 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.5796 (mpt) REVERT: E 75 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7299 (ttm110) REVERT: E 97 ASP cc_start: 0.8150 (m-30) cc_final: 0.7578 (t0) REVERT: E 120 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7925 (ttpp) REVERT: E 130 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7879 (t0) REVERT: E 207 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7672 (tp30) REVERT: E 225 CYS cc_start: 0.7377 (t) cc_final: 0.7037 (t) REVERT: E 229 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7791 (mmt90) REVERT: E 262 MET cc_start: 0.4226 (mpp) cc_final: 0.3826 (mpp) REVERT: E 391 MET cc_start: 0.6872 (mtp) cc_final: 0.6569 (tmm) REVERT: E 420 PHE cc_start: 0.7544 (t80) cc_final: 0.7282 (t80) outliers start: 87 outliers final: 38 residues processed: 325 average time/residue: 0.5313 time to fit residues: 191.4046 Evaluate side-chains 323 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN D 282 GLN B 219 ASN C 219 ASN E 219 ASN E 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116229 restraints weight = 15269.495| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.23 r_work: 0.3210 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14470 Z= 0.158 Angle : 0.713 9.734 19675 Z= 0.358 Chirality : 0.046 0.170 2260 Planarity : 0.004 0.039 2430 Dihedral : 5.905 47.928 2185 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.88 % Allowed : 19.21 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -1.60 (0.20), residues: 1710 helix: -1.03 (0.22), residues: 575 sheet: 0.00 (0.28), residues: 370 loop : -1.54 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.013 0.002 TYR A 144 PHE 0.013 0.001 PHE A 115 TRP 0.035 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00376 (14445) covalent geometry : angle 0.69449 (19610) SS BOND : bond 0.00267 ( 10) SS BOND : angle 4.71486 ( 20) hydrogen bonds : bond 0.03810 ( 532) hydrogen bonds : angle 4.58317 ( 1968) link_BETA1-4 : bond 0.00462 ( 10) link_BETA1-4 : angle 1.80840 ( 30) link_NAG-ASN : bond 0.00119 ( 5) link_NAG-ASN : angle 0.33096 ( 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 357 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 0.505 Fit side-chains REVERT: A 28 GLU cc_start: 0.7696 (tp30) cc_final: 0.7039 (tp30) REVERT: A 75 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7357 (ttm110) REVERT: A 97 ASP cc_start: 0.7965 (m-30) cc_final: 0.7462 (t0) REVERT: A 225 CYS cc_start: 0.7484 (t) cc_final: 0.7179 (t) REVERT: A 227 GLU cc_start: 0.8577 (pt0) cc_final: 0.8213 (tt0) REVERT: A 243 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.5961 (mpt) REVERT: A 292 LYS cc_start: 0.8130 (mttt) cc_final: 0.7795 (mttp) REVERT: A 391 MET cc_start: 0.6981 (mtp) cc_final: 0.6652 (tmm) REVERT: A 420 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: D 75 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7425 (ttm110) REVERT: D 207 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7574 (tp30) REVERT: D 210 ASP cc_start: 0.7970 (m-30) cc_final: 0.7700 (m-30) REVERT: D 229 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7516 (mmt90) REVERT: D 243 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6189 (mpt) REVERT: D 292 LYS cc_start: 0.8181 (mttt) cc_final: 0.7894 (mttp) REVERT: D 391 MET cc_start: 0.6822 (mtp) cc_final: 0.6522 (ttp) REVERT: D 420 PHE cc_start: 0.7531 (t80) cc_final: 0.7237 (t80) REVERT: B 28 GLU cc_start: 0.7809 (tp30) cc_final: 0.7028 (tp30) REVERT: B 97 ASP cc_start: 0.8040 (m-30) cc_final: 0.7528 (t0) REVERT: B 126 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7113 (pm20) REVERT: B 207 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7618 (tp30) REVERT: B 210 ASP cc_start: 0.8035 (m-30) cc_final: 0.7709 (m-30) REVERT: B 243 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6007 (mpt) REVERT: B 260 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.5062 (pt) REVERT: C 28 GLU cc_start: 0.7663 (tp30) cc_final: 0.7024 (tp30) REVERT: C 49 LYS cc_start: 0.8665 (mttt) cc_final: 0.8146 (mmtt) REVERT: C 75 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7245 (ttm110) REVERT: C 94 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6891 (t80) REVERT: C 97 ASP cc_start: 0.7907 (m-30) cc_final: 0.7304 (t0) REVERT: C 156 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.6497 (mmt) REVERT: C 229 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7464 (mmt90) REVERT: C 243 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5778 (mpt) REVERT: E 75 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7272 (ttm110) REVERT: E 97 ASP cc_start: 0.8148 (m-30) cc_final: 0.7636 (t0) REVERT: E 120 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7818 (ttpp) REVERT: E 130 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7835 (t0) REVERT: E 225 CYS cc_start: 0.7368 (t) cc_final: 0.7059 (t) REVERT: E 229 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7600 (mmt90) REVERT: E 243 MET cc_start: 0.7438 (mmt) cc_final: 0.7003 (mtt) REVERT: E 262 MET cc_start: 0.4195 (mpp) cc_final: 0.3818 (mpp) REVERT: E 391 MET cc_start: 0.6841 (mtp) cc_final: 0.6530 (tmm) REVERT: E 418 ASN cc_start: 0.7249 (m-40) cc_final: 0.7025 (m110) REVERT: E 420 PHE cc_start: 0.7495 (t80) cc_final: 0.7232 (t80) outliers start: 74 outliers final: 34 residues processed: 318 average time/residue: 0.4997 time to fit residues: 176.5897 Evaluate side-chains 316 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 219 ASN D 219 ASN B 219 ASN B 282 GLN C 219 ASN E 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121799 restraints weight = 15189.831| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.24 r_work: 0.3226 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14470 Z= 0.140 Angle : 0.705 11.525 19675 Z= 0.353 Chirality : 0.045 0.184 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.738 47.519 2185 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.89 % Allowed : 20.46 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -1.42 (0.20), residues: 1710 helix: -0.83 (0.22), residues: 580 sheet: 0.03 (0.29), residues: 370 loop : -1.44 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.016 0.002 TYR D 213 PHE 0.011 0.001 PHE A 115 TRP 0.037 0.001 TRP E 255 HIS 0.003 0.000 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00328 (14445) covalent geometry : angle 0.68857 (19610) SS BOND : bond 0.00284 ( 10) SS BOND : angle 4.46564 ( 20) hydrogen bonds : bond 0.03688 ( 532) hydrogen bonds : angle 4.50210 ( 1968) link_BETA1-4 : bond 0.00443 ( 10) link_BETA1-4 : angle 1.67567 ( 30) link_NAG-ASN : bond 0.00133 ( 5) link_NAG-ASN : angle 0.33527 ( 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 346 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 0.537 Fit side-chains REVERT: A 75 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7387 (ttm110) REVERT: A 97 ASP cc_start: 0.7946 (m-30) cc_final: 0.7455 (t0) REVERT: A 156 MET cc_start: 0.8352 (mmt) cc_final: 0.7857 (mmt) REVERT: A 225 CYS cc_start: 0.7449 (t) cc_final: 0.7209 (t) REVERT: A 227 GLU cc_start: 0.8561 (pt0) cc_final: 0.8273 (tt0) REVERT: A 292 LYS cc_start: 0.8096 (mttt) cc_final: 0.7763 (mttp) REVERT: A 391 MET cc_start: 0.6974 (mtp) cc_final: 0.6695 (tmm) REVERT: A 420 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: D 75 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7436 (ttm110) REVERT: D 97 ASP cc_start: 0.7893 (m-30) cc_final: 0.7384 (t0) REVERT: D 101 LEU cc_start: 0.7712 (mt) cc_final: 0.7501 (mm) REVERT: D 210 ASP cc_start: 0.7934 (m-30) cc_final: 0.7685 (m-30) REVERT: D 225 CYS cc_start: 0.7533 (t) cc_final: 0.7244 (t) REVERT: D 227 GLU cc_start: 0.8710 (pt0) cc_final: 0.8480 (pt0) REVERT: D 229 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7323 (mmt90) REVERT: D 243 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6205 (mpt) REVERT: D 292 LYS cc_start: 0.8145 (mttt) cc_final: 0.7873 (mttp) REVERT: D 391 MET cc_start: 0.6805 (mtp) cc_final: 0.6581 (tmm) REVERT: D 420 PHE cc_start: 0.7519 (t80) cc_final: 0.7235 (t80) REVERT: B 28 GLU cc_start: 0.7824 (tp30) cc_final: 0.7052 (tp30) REVERT: B 97 ASP cc_start: 0.7996 (m-30) cc_final: 0.7542 (t0) REVERT: B 126 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7084 (pm20) REVERT: B 207 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7596 (tp30) REVERT: B 210 ASP cc_start: 0.8046 (m-30) cc_final: 0.7726 (m-30) REVERT: B 229 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8009 (mtp85) REVERT: B 243 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5942 (mpt) REVERT: C 28 GLU cc_start: 0.7664 (tp30) cc_final: 0.7031 (tp30) REVERT: C 49 LYS cc_start: 0.8669 (mttt) cc_final: 0.8156 (mmtt) REVERT: C 75 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7246 (ttm110) REVERT: C 94 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.6928 (t80) REVERT: C 97 ASP cc_start: 0.7896 (m-30) cc_final: 0.7300 (t0) REVERT: C 101 LEU cc_start: 0.7845 (mt) cc_final: 0.7595 (mm) REVERT: C 156 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.6461 (mmt) REVERT: C 227 GLU cc_start: 0.8565 (pt0) cc_final: 0.8347 (tt0) REVERT: C 243 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.5714 (mpt) REVERT: C 418 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7157 (m110) REVERT: E 75 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7262 (ttm110) REVERT: E 97 ASP cc_start: 0.8085 (m-30) cc_final: 0.7640 (t0) REVERT: E 101 LEU cc_start: 0.7524 (mt) cc_final: 0.7266 (mm) REVERT: E 120 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (ttpp) REVERT: E 130 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7828 (t0) REVERT: E 225 CYS cc_start: 0.7399 (t) cc_final: 0.7120 (t) REVERT: E 229 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7599 (mmt90) REVERT: E 243 MET cc_start: 0.7412 (mmt) cc_final: 0.7018 (mtt) REVERT: E 262 MET cc_start: 0.4210 (mpp) cc_final: 0.3835 (mpp) REVERT: E 391 MET cc_start: 0.6851 (mtp) cc_final: 0.6514 (tmm) REVERT: E 418 ASN cc_start: 0.7266 (m-40) cc_final: 0.7030 (m110) REVERT: E 420 PHE cc_start: 0.7415 (t80) cc_final: 0.7181 (t80) outliers start: 59 outliers final: 25 residues processed: 314 average time/residue: 0.5285 time to fit residues: 184.1085 Evaluate side-chains 316 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 219 ASN D 180 ASN D 219 ASN B 219 ASN B 282 GLN C 219 ASN C 282 GLN E 219 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120209 restraints weight = 15586.462| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.21 r_work: 0.3158 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14470 Z= 0.176 Angle : 0.730 10.531 19675 Z= 0.365 Chirality : 0.046 0.169 2260 Planarity : 0.004 0.037 2430 Dihedral : 5.758 48.444 2185 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.29 % Allowed : 20.40 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -1.28 (0.20), residues: 1710 helix: -0.63 (0.22), residues: 575 sheet: 0.06 (0.28), residues: 370 loop : -1.41 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 229 TYR 0.013 0.002 TYR C 317 PHE 0.013 0.001 PHE A 115 TRP 0.032 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00423 (14445) covalent geometry : angle 0.71345 (19610) SS BOND : bond 0.00275 ( 10) SS BOND : angle 4.59322 ( 20) hydrogen bonds : bond 0.03814 ( 532) hydrogen bonds : angle 4.50579 ( 1968) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.66602 ( 30) link_NAG-ASN : bond 0.00074 ( 5) link_NAG-ASN : angle 0.35772 ( 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 354 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 0.541 Fit side-chains REVERT: A 75 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: A 97 ASP cc_start: 0.7928 (m-30) cc_final: 0.7461 (t0) REVERT: A 227 GLU cc_start: 0.8590 (pt0) cc_final: 0.8297 (tt0) REVERT: A 391 MET cc_start: 0.7072 (mtp) cc_final: 0.6801 (tmm) REVERT: A 420 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: D 75 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7405 (ttm110) REVERT: D 101 LEU cc_start: 0.7697 (mt) cc_final: 0.7482 (mm) REVERT: D 210 ASP cc_start: 0.7971 (m-30) cc_final: 0.7697 (m-30) REVERT: D 225 CYS cc_start: 0.7478 (t) cc_final: 0.7191 (t) REVERT: D 227 GLU cc_start: 0.8705 (pt0) cc_final: 0.8503 (pt0) REVERT: D 229 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7376 (mmt90) REVERT: D 243 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6229 (mpt) REVERT: D 292 LYS cc_start: 0.8218 (mttt) cc_final: 0.7945 (mttp) REVERT: D 391 MET cc_start: 0.6838 (mtp) cc_final: 0.6625 (tmm) REVERT: D 420 PHE cc_start: 0.7501 (t80) cc_final: 0.7195 (t80) REVERT: B 28 GLU cc_start: 0.7818 (tp30) cc_final: 0.7053 (tp30) REVERT: B 97 ASP cc_start: 0.7993 (m-30) cc_final: 0.7524 (t0) REVERT: B 126 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7124 (pm20) REVERT: B 207 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7658 (tp30) REVERT: B 210 ASP cc_start: 0.8020 (m-30) cc_final: 0.7691 (m-30) REVERT: B 229 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: B 243 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6040 (mpt) REVERT: C 28 GLU cc_start: 0.7686 (tp30) cc_final: 0.7056 (tp30) REVERT: C 49 LYS cc_start: 0.8690 (mttt) cc_final: 0.8188 (mmtt) REVERT: C 75 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7196 (ttm110) REVERT: C 94 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6964 (t80) REVERT: C 96 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: C 97 ASP cc_start: 0.7873 (m-30) cc_final: 0.7254 (t0) REVERT: C 101 LEU cc_start: 0.7819 (mt) cc_final: 0.7566 (mm) REVERT: C 156 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.6570 (mmt) REVERT: C 227 GLU cc_start: 0.8567 (pt0) cc_final: 0.8341 (tt0) REVERT: C 243 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.5743 (mpt) REVERT: E 75 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7209 (ttm110) REVERT: E 97 ASP cc_start: 0.8079 (m-30) cc_final: 0.7643 (t0) REVERT: E 101 LEU cc_start: 0.7518 (mt) cc_final: 0.7273 (mm) REVERT: E 102 ASP cc_start: 0.8625 (t70) cc_final: 0.8357 (t70) REVERT: E 120 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7784 (ttpp) REVERT: E 130 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7815 (t0) REVERT: E 156 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7598 (mmm) REVERT: E 207 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7660 (tp30) REVERT: E 225 CYS cc_start: 0.7327 (t) cc_final: 0.7066 (t) REVERT: E 229 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7592 (mmt90) REVERT: E 262 MET cc_start: 0.4289 (mpp) cc_final: 0.3914 (mpp) REVERT: E 391 MET cc_start: 0.6910 (mtp) cc_final: 0.6612 (tmm) REVERT: E 415 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6107 (tm) REVERT: E 418 ASN cc_start: 0.7271 (m-40) cc_final: 0.7039 (m110) REVERT: E 420 PHE cc_start: 0.7307 (t80) cc_final: 0.7099 (t80) outliers start: 65 outliers final: 33 residues processed: 317 average time/residue: 0.5123 time to fit residues: 179.9636 Evaluate side-chains 323 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 125 optimal weight: 0.1980 chunk 91 optimal weight: 0.0770 chunk 156 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 219 ASN D 219 ASN B 219 ASN B 282 GLN C 219 ASN E 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123766 restraints weight = 15529.604| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.24 r_work: 0.3197 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14470 Z= 0.126 Angle : 0.697 10.829 19675 Z= 0.347 Chirality : 0.045 0.173 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.552 47.566 2185 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.23 % Allowed : 22.24 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -1.10 (0.20), residues: 1710 helix: -0.37 (0.22), residues: 575 sheet: 0.21 (0.28), residues: 375 loop : -1.45 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.011 0.001 TYR E 317 PHE 0.015 0.001 PHE A 115 TRP 0.030 0.001 TRP E 255 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00296 (14445) covalent geometry : angle 0.68381 (19610) SS BOND : bond 0.00355 ( 10) SS BOND : angle 4.04359 ( 20) hydrogen bonds : bond 0.03560 ( 532) hydrogen bonds : angle 4.41911 ( 1968) link_BETA1-4 : bond 0.00435 ( 10) link_BETA1-4 : angle 1.52897 ( 30) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 0.31661 ( 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 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.566 Fit side-chains REVERT: A 49 LYS cc_start: 0.8592 (mttm) cc_final: 0.8252 (mmtt) REVERT: A 75 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7351 (ttm110) REVERT: A 97 ASP cc_start: 0.7909 (m-30) cc_final: 0.7458 (t0) REVERT: A 156 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7922 (mmm) REVERT: A 227 GLU cc_start: 0.8459 (pt0) cc_final: 0.8231 (tt0) REVERT: A 292 LYS cc_start: 0.8066 (mttt) cc_final: 0.7750 (mttp) REVERT: A 391 MET cc_start: 0.7052 (mtp) cc_final: 0.6765 (tmm) REVERT: A 420 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: D 75 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7392 (ttm110) REVERT: D 130 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7561 (t0) REVERT: D 210 ASP cc_start: 0.7957 (m-30) cc_final: 0.7626 (m-30) REVERT: D 225 CYS cc_start: 0.7412 (t) cc_final: 0.7145 (t) REVERT: D 229 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7863 (mmt90) REVERT: D 243 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6194 (mpt) REVERT: D 292 LYS cc_start: 0.8039 (mttt) cc_final: 0.7773 (mttp) REVERT: D 391 MET cc_start: 0.6796 (mtp) cc_final: 0.6556 (tmm) REVERT: D 420 PHE cc_start: 0.7475 (t80) cc_final: 0.7179 (t80) REVERT: B 28 GLU cc_start: 0.7788 (tp30) cc_final: 0.7062 (tp30) REVERT: B 97 ASP cc_start: 0.7917 (m-30) cc_final: 0.7488 (t0) REVERT: B 126 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7124 (pm20) REVERT: B 207 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7594 (tp30) REVERT: B 210 ASP cc_start: 0.8023 (m-30) cc_final: 0.7713 (m-30) REVERT: B 229 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: C 28 GLU cc_start: 0.7640 (tp30) cc_final: 0.7003 (tp30) REVERT: C 49 LYS cc_start: 0.8710 (mttt) cc_final: 0.8201 (mmtt) REVERT: C 75 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7181 (ttm110) REVERT: C 94 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6922 (t80) REVERT: C 96 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: C 97 ASP cc_start: 0.7849 (m-30) cc_final: 0.7224 (t0) REVERT: C 101 LEU cc_start: 0.7773 (mt) cc_final: 0.7526 (mm) REVERT: E 75 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7203 (ttm110) REVERT: E 97 ASP cc_start: 0.8006 (m-30) cc_final: 0.7600 (t0) REVERT: E 101 LEU cc_start: 0.7518 (mt) cc_final: 0.7276 (mm) REVERT: E 102 ASP cc_start: 0.8578 (t70) cc_final: 0.8320 (t70) REVERT: E 120 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7659 (ttpp) REVERT: E 130 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7780 (t0) REVERT: E 156 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7506 (mmm) REVERT: E 225 CYS cc_start: 0.7309 (t) cc_final: 0.7100 (t) REVERT: E 229 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7576 (mmt90) REVERT: E 262 MET cc_start: 0.4149 (mpp) cc_final: 0.3797 (mpp) REVERT: E 391 MET cc_start: 0.6851 (mtp) cc_final: 0.6540 (tmm) outliers start: 49 outliers final: 29 residues processed: 299 average time/residue: 0.5166 time to fit residues: 170.6950 Evaluate side-chains 312 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 91 optimal weight: 0.2980 chunk 144 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 58 ASN D 219 ASN B 219 ASN C 171 GLN C 219 ASN E 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123805 restraints weight = 15389.148| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.17 r_work: 0.3245 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14470 Z= 0.112 Angle : 0.687 12.447 19675 Z= 0.337 Chirality : 0.044 0.157 2260 Planarity : 0.004 0.030 2430 Dihedral : 5.347 47.722 2185 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.44 % Allowed : 23.23 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -0.88 (0.20), residues: 1710 helix: -0.09 (0.22), residues: 580 sheet: 0.30 (0.28), residues: 375 loop : -1.39 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.010 0.001 TYR E 317 PHE 0.011 0.001 PHE A 115 TRP 0.029 0.001 TRP E 255 HIS 0.002 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00255 (14445) covalent geometry : angle 0.67524 (19610) SS BOND : bond 0.00266 ( 10) SS BOND : angle 3.74862 ( 20) hydrogen bonds : bond 0.03349 ( 532) hydrogen bonds : angle 4.27859 ( 1968) link_BETA1-4 : bond 0.00365 ( 10) link_BETA1-4 : angle 1.40784 ( 30) link_NAG-ASN : bond 0.00164 ( 5) link_NAG-ASN : angle 0.40902 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.30 seconds wall clock time: 81 minutes 55.96 seconds (4915.96 seconds total)