Starting phenix.real_space_refine on Sat Sep 12 06:30:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm6_20389/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm6_20389/09_2026/6pm6_20389.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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: 2.92, per 1000 atoms: 0.21 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: 0.99 Conformation dependent library (CDL) restraints added in 634.5 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: 0.49 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: 2.15 Time building geometry restraints manager: 1.36 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 - 14.96: 8044 14.96 - 29.93: 392 29.93 - 44.89: 64 44.89 - 59.85: 0 59.85 - 74.82: 10 Dihedral angle restraints: 8510 sinusoidal: 3395 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 8507 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 9.390 74.817 5160 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/Z covalent geometry : bond 0.00470 / 0.23 (14445) covalent geometry : angle 0.92210 / 0.48 (19610) SS BOND : bond 0.00558 / 0.30 ( 10) SS BOND : angle 2.83241 / 1.71 ( 20) hydrogen bonds : bond 0.28789 / 18.92 ( 532) hydrogen bonds : angle 9.72342 / 6.61 ( 1968) link_BETA1-4 : bond 0.00525 / 0.31 ( 10) link_BETA1-4 : angle 1.85193 / 1.19 ( 30) link_NAG-ASN : bond 0.00105 / 0.06 ( 5) link_NAG-ASN : angle 1.66344 / 0.94 ( 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 : 0.506 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: 0.4701 time to fit residues: 210.4244 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 : 0.423 ------------------------------------------------------------------------------- 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... 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.163449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125053 restraints weight = 15631.025| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.12 r_work: 0.3188 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2045 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= 0.152 Angle : 0.782 14.400 19675 Z= 0.401 Chirality : 0.049 0.316 2260 Planarity : 0.005 0.053 2430 Dihedral : 5.968 30.416 1880 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.64 % Allowed : 11.16 % Favored : 86.20 % 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: -3.60 (0.17), residues: 1710 helix: -3.10 (0.15), residues: 565 sheet: -1.07 (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 0.016 0.002 TYR B 317 PHE 0.013 0.001 PHE D 309 TRP 0.009 0.001 TRP A 422 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14445) covalent geometry : angle 0.76287 / 0.39 (19610) SS BOND : bond 0.01158 / 0.62 ( 10) SS BOND : angle 5.24710 / 3.08 ( 20) hydrogen bonds : bond 0.05871 / 3.84 ( 532) hydrogen bonds : angle 6.02485 / 4.01 ( 1968) link_BETA1-4 : bond 0.00464 / 0.28 ( 10) link_BETA1-4 : angle 1.40247 / 0.85 ( 30) link_NAG-ASN : bond 0.00254 / 0.14 ( 5) link_NAG-ASN : angle 0.52491 / 0.29 ( 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 351 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7162 (ttm-80) cc_final: 0.6524 (ttm110) REVERT: A 96 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7140 (t0) REVERT: A 97 ASP cc_start: 0.7468 (m-30) cc_final: 0.6982 (t0) REVERT: A 206 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7538 (mttt) REVERT: A 212 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.7159 (ptp-110) REVERT: A 262 MET cc_start: 0.3575 (mpp) cc_final: 0.3324 (mpp) REVERT: A 292 LYS cc_start: 0.7355 (mttt) cc_final: 0.7069 (mttp) REVERT: A 391 MET cc_start: 0.6788 (mtp) cc_final: 0.6344 (tmm) REVERT: A 420 PHE cc_start: 0.7676 (t80) cc_final: 0.6913 (t80) REVERT: D 75 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6615 (ttm110) REVERT: D 206 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7538 (mtmm) REVERT: D 243 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.5881 (mpt) REVERT: D 292 LYS cc_start: 0.7387 (mttt) cc_final: 0.7143 (mttp) REVERT: D 303 MET cc_start: 0.8812 (mmt) cc_final: 0.8569 (mmt) REVERT: D 391 MET cc_start: 0.6820 (mtp) cc_final: 0.6385 (ttp) REVERT: B 43 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8253 (mtp-110) REVERT: B 222 LYS cc_start: 0.7025 (ptmm) cc_final: 0.6604 (pttt) REVERT: B 243 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5554 (mpt) REVERT: B 292 LYS cc_start: 0.7293 (mttt) cc_final: 0.7034 (mttp) REVERT: B 401 ARG cc_start: 0.4745 (tpt170) cc_final: 0.4493 (tpt-90) REVERT: B 420 PHE cc_start: 0.7772 (t80) cc_final: 0.7289 (t80) REVERT: C 75 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6718 (mtp-110) REVERT: C 96 ASP cc_start: 0.7845 (t0) cc_final: 0.7525 (t0) REVERT: C 97 ASP cc_start: 0.7304 (m-30) cc_final: 0.6619 (t0) REVERT: C 105 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: C 206 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7308 (mtmm) REVERT: C 243 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5659 (mpt) REVERT: C 401 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.4985 (tmt90) REVERT: C 420 PHE cc_start: 0.7350 (t80) cc_final: 0.7074 (t80) REVERT: E 75 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.6797 (ttm110) REVERT: E 96 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7092 (t0) REVERT: E 97 ASP cc_start: 0.7672 (m-30) cc_final: 0.7076 (t0) REVERT: E 206 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7546 (mmmm) REVERT: E 210 ASP cc_start: 0.7836 (m-30) cc_final: 0.6904 (t0) REVERT: E 243 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.5696 (mpt) REVERT: E 262 MET cc_start: 0.3955 (mpp) cc_final: 0.3435 (mpp) REVERT: E 391 MET cc_start: 0.6881 (mtp) cc_final: 0.6423 (ttp) outliers start: 40 outliers final: 13 residues processed: 335 average time/residue: 0.4822 time to fit residues: 179.3907 Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET 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 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: 3.9990 chunk 143 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3756 r_free = 0.3756 target = 0.154144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115703 restraints weight = 16080.984| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.97 r_work: 0.3112 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 14470 Z= 0.279 Angle : 0.847 13.793 19675 Z= 0.432 Chirality : 0.051 0.284 2260 Planarity : 0.005 0.047 2430 Dihedral : 6.011 28.949 1880 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.54 % Allowed : 13.33 % Favored : 81.12 % 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: -2.84 (0.18), residues: 1710 helix: -2.28 (0.19), residues: 555 sheet: -0.64 (0.27), residues: 395 loop : -2.17 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 212 TYR 0.017 0.003 TYR A 144 PHE 0.018 0.002 PHE B 124 TRP 0.019 0.003 TRP B 302 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.28 (14445) covalent geometry : angle 0.83001 / 0.42 (19610) SS BOND : bond 0.00944 / 0.52 ( 10) SS BOND : angle 5.15804 / 2.99 ( 20) hydrogen bonds : bond 0.05062 / 3.34 ( 532) hydrogen bonds : angle 5.36259 / 3.58 ( 1968) link_BETA1-4 : bond 0.00570 / 0.31 ( 10) link_BETA1-4 : angle 1.50096 / 0.95 ( 30) link_NAG-ASN : bond 0.00062 / 0.03 ( 5) link_NAG-ASN : angle 0.53742 / 0.33 ( 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 377 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 293 time to evaluate : 0.515 Fit side-chains REVERT: A 49 LYS cc_start: 0.8678 (mttt) cc_final: 0.8263 (mtpt) REVERT: A 75 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.6863 (ttm110) REVERT: A 292 LYS cc_start: 0.7754 (mttt) cc_final: 0.7436 (mttp) REVERT: A 391 MET cc_start: 0.6951 (mtp) cc_final: 0.6624 (tmm) REVERT: A 420 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7005 (t80) REVERT: D 75 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.6829 (ttm110) REVERT: D 97 ASP cc_start: 0.7670 (m-30) cc_final: 0.7049 (t0) REVERT: D 206 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7698 (mtmm) REVERT: D 207 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7528 (tp30) REVERT: D 210 ASP cc_start: 0.7819 (m-30) cc_final: 0.7405 (m-30) REVERT: D 292 LYS cc_start: 0.7909 (mttt) cc_final: 0.7692 (mttm) REVERT: D 391 MET cc_start: 0.6838 (mtp) cc_final: 0.6480 (ttp) REVERT: B 96 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7470 (t0) REVERT: B 97 ASP cc_start: 0.7763 (m-30) cc_final: 0.7151 (t0) REVERT: B 243 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.5682 (mpt) REVERT: B 420 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7276 (t80) REVERT: C 28 GLU cc_start: 0.7493 (tp30) cc_final: 0.6914 (tp30) REVERT: C 75 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.6819 (ttm110) REVERT: C 96 ASP cc_start: 0.7963 (t0) cc_final: 0.7701 (t0) REVERT: C 97 ASP cc_start: 0.7597 (m-30) cc_final: 0.6853 (t0) REVERT: C 105 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7175 (mmp) REVERT: C 227 GLU cc_start: 0.8478 (pt0) cc_final: 0.8204 (pt0) REVERT: C 243 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.5914 (mpt) REVERT: C 401 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5187 (tmt90) REVERT: C 420 PHE cc_start: 0.7417 (t80) cc_final: 0.7161 (t80) REVERT: E 75 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.6881 (ttm110) REVERT: E 96 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7367 (t0) REVERT: E 97 ASP cc_start: 0.7874 (m-30) cc_final: 0.7165 (t0) REVERT: E 173 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7736 (mt-10) REVERT: E 206 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7774 (mtmm) REVERT: E 207 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7679 (tp30) REVERT: E 210 ASP cc_start: 0.7955 (m-30) cc_final: 0.7280 (m-30) REVERT: E 227 GLU cc_start: 0.8343 (pt0) cc_final: 0.8008 (pt0) REVERT: E 262 MET cc_start: 0.3982 (mpp) cc_final: 0.3577 (mpp) REVERT: E 391 MET cc_start: 0.6839 (mtp) cc_final: 0.6490 (ttp) outliers start: 84 outliers final: 34 residues processed: 336 average time/residue: 0.4444 time to fit residues: 166.9819 Evaluate side-chains 318 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 130 ASP 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 63 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain B residue 44 ILE 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 138 LYS 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 104 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 168 CYS 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 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 167 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 199 THR 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: 1.9990 chunk 93 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 141 ASN A 282 GLN D 58 ASN D 85 ASN D 141 ASN D 219 ASN B 219 ASN C 219 ASN E 58 ASN E 62 ASN E 85 ASN E 141 ASN E 219 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119935 restraints weight = 15892.916| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.96 r_work: 0.3215 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3231 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= 0.140 Angle : 0.693 10.306 19675 Z= 0.352 Chirality : 0.046 0.199 2260 Planarity : 0.004 0.041 2430 Dihedral : 5.541 33.076 1880 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.69 % Allowed : 16.96 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.23 (0.19), residues: 1710 helix: -1.74 (0.20), residues: 555 sheet: 0.33 (0.30), residues: 320 loop : -2.03 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 229 TYR 0.013 0.002 TYR A 144 PHE 0.011 0.001 PHE E 414 TRP 0.023 0.002 TRP E 255 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (14445) covalent geometry : angle 0.67777 / 0.35 (19610) SS BOND : bond 0.00402 / 0.23 ( 10) SS BOND : angle 4.23841 / 2.45 ( 20) hydrogen bonds : bond 0.04076 / 2.67 ( 532) hydrogen bonds : angle 4.88364 / 3.24 ( 1968) link_BETA1-4 : bond 0.00463 / 0.26 ( 10) link_BETA1-4 : angle 1.55808 / 0.96 ( 30) link_NAG-ASN : bond 0.00147 / 0.08 ( 5) link_NAG-ASN : angle 0.26164 / 0.15 ( 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 371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 300 time to evaluate : 0.517 Fit side-chains REVERT: A 75 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.6994 (ttm110) REVERT: A 97 ASP cc_start: 0.7645 (m-30) cc_final: 0.7048 (t0) REVERT: A 243 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.5966 (mpt) REVERT: A 292 LYS cc_start: 0.7756 (mttt) cc_final: 0.7452 (mttp) REVERT: A 391 MET cc_start: 0.6948 (mtp) cc_final: 0.6634 (tmm) REVERT: A 420 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7007 (t80) REVERT: D 75 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7209 (ttm110) REVERT: D 97 ASP cc_start: 0.7713 (m-30) cc_final: 0.7107 (t0) REVERT: D 206 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7770 (mtmm) REVERT: D 207 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7513 (tp30) REVERT: D 227 GLU cc_start: 0.8267 (pt0) cc_final: 0.7962 (pt0) REVERT: D 391 MET cc_start: 0.6841 (mtp) cc_final: 0.6504 (ttp) REVERT: D 420 PHE cc_start: 0.7308 (t80) cc_final: 0.7104 (t80) REVERT: B 96 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7469 (t0) REVERT: B 97 ASP cc_start: 0.7744 (m-30) cc_final: 0.7108 (t0) REVERT: B 102 ASP cc_start: 0.8274 (t70) cc_final: 0.8023 (t70) REVERT: B 227 GLU cc_start: 0.8238 (pt0) cc_final: 0.7760 (pt0) REVERT: C 28 GLU cc_start: 0.7493 (tp30) cc_final: 0.6869 (tp30) REVERT: C 75 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7067 (ttm110) REVERT: C 96 ASP cc_start: 0.7921 (t0) cc_final: 0.7686 (t0) REVERT: C 97 ASP cc_start: 0.7626 (m-30) cc_final: 0.6907 (t0) REVERT: C 156 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6547 (mmt) REVERT: C 163 MET cc_start: 0.7999 (mtm) cc_final: 0.7766 (mpp) REVERT: C 243 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.5682 (mpt) REVERT: C 401 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.5182 (tmt90) REVERT: C 420 PHE cc_start: 0.7396 (t80) cc_final: 0.7185 (m-80) REVERT: E 75 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7091 (ttm110) REVERT: E 97 ASP cc_start: 0.7824 (m-30) cc_final: 0.7197 (t0) REVERT: E 130 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7635 (t0) REVERT: E 156 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.6526 (mmt) REVERT: E 206 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7793 (mtmm) REVERT: E 207 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7642 (tp30) REVERT: E 229 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7475 (mmt90) REVERT: E 262 MET cc_start: 0.4190 (mpp) cc_final: 0.3842 (mpp) REVERT: E 391 MET cc_start: 0.6842 (mtp) cc_final: 0.6501 (ttp) REVERT: E 420 PHE cc_start: 0.7373 (t80) cc_final: 0.7132 (t80) outliers start: 71 outliers final: 19 residues processed: 332 average time/residue: 0.4380 time to fit residues: 162.7213 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 243 MET 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 269 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN 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 171 GLN 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 E residue 63 SER Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 168 CYS 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: 0.9990 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN A 231 HIS D 219 ASN D 282 GLN B 219 ASN C 219 ASN E 77 ASN E 219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121414 restraints weight = 15807.301| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.94 r_work: 0.3205 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3468 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= 0.128 Angle : 0.668 8.580 19675 Z= 0.338 Chirality : 0.045 0.164 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.408 42.478 1880 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.49 % Allowed : 17.69 % Favored : 77.82 % 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: -1.91 (0.19), residues: 1710 helix: -1.37 (0.21), residues: 575 sheet: 0.44 (0.30), residues: 320 loop : -1.88 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.014 0.002 TYR B 317 PHE 0.014 0.001 PHE E 414 TRP 0.027 0.001 TRP E 255 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14445) covalent geometry : angle 0.65468 / 0.33 (19610) SS BOND : bond 0.00309 / 0.18 ( 10) SS BOND : angle 3.83033 / 2.14 ( 20) hydrogen bonds : bond 0.03869 / 2.54 ( 532) hydrogen bonds : angle 4.66470 / 3.09 ( 1968) link_BETA1-4 : bond 0.00466 / 0.27 ( 10) link_BETA1-4 : angle 1.51185 / 0.94 ( 30) link_NAG-ASN : bond 0.00131 / 0.07 ( 5) link_NAG-ASN : angle 0.29862 / 0.18 ( 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 367 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 0.543 Fit side-chains REVERT: A 75 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7004 (ttm110) REVERT: A 156 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7198 (mmt) REVERT: A 243 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5764 (mpt) REVERT: A 260 ILE cc_start: 0.4831 (OUTLIER) cc_final: 0.4601 (pt) REVERT: A 292 LYS cc_start: 0.7695 (mttt) cc_final: 0.7397 (mttp) REVERT: A 391 MET cc_start: 0.6934 (mtp) cc_final: 0.6609 (tmm) REVERT: A 420 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: D 75 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7086 (ttm110) REVERT: D 97 ASP cc_start: 0.7620 (m-30) cc_final: 0.7069 (t0) REVERT: D 206 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7720 (mtmm) REVERT: D 207 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7512 (tp30) REVERT: D 391 MET cc_start: 0.6819 (mtp) cc_final: 0.6490 (ttp) REVERT: D 420 PHE cc_start: 0.7270 (t80) cc_final: 0.6978 (t80) REVERT: B 28 GLU cc_start: 0.7672 (tp30) cc_final: 0.6938 (tp30) REVERT: B 97 ASP cc_start: 0.7747 (m-30) cc_final: 0.7166 (t0) REVERT: B 102 ASP cc_start: 0.8280 (t70) cc_final: 0.7924 (t70) REVERT: B 126 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6803 (pm20) REVERT: B 207 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7500 (tp30) REVERT: B 210 ASP cc_start: 0.7799 (m-30) cc_final: 0.7449 (m-30) REVERT: B 243 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.5586 (mpt) REVERT: C 28 GLU cc_start: 0.7468 (tp30) cc_final: 0.6862 (tp30) REVERT: C 49 LYS cc_start: 0.8513 (mttt) cc_final: 0.7991 (mmtt) REVERT: C 75 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.6914 (ttm110) REVERT: C 96 ASP cc_start: 0.7910 (t0) cc_final: 0.7705 (t0) REVERT: C 97 ASP cc_start: 0.7645 (m-30) cc_final: 0.7043 (t0) REVERT: C 156 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.6370 (mmt) REVERT: C 173 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 188 GLU cc_start: 0.8547 (mp0) cc_final: 0.8299 (mp0) REVERT: C 229 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7254 (mmt90) REVERT: C 243 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.5436 (mpt) REVERT: C 391 MET cc_start: 0.4600 (tmm) cc_final: 0.4157 (tmm) REVERT: C 401 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.5192 (tmt90) REVERT: C 420 PHE cc_start: 0.7415 (t80) cc_final: 0.7186 (m-80) REVERT: E 75 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.6945 (ttm110) REVERT: E 96 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7401 (t0) REVERT: E 97 ASP cc_start: 0.7760 (m-30) cc_final: 0.7225 (t0) REVERT: E 130 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7552 (t0) REVERT: E 206 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7649 (mmmm) REVERT: E 207 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7563 (tp30) REVERT: E 229 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7278 (mmt90) REVERT: E 262 MET cc_start: 0.4220 (mpp) cc_final: 0.3751 (mpp) REVERT: E 391 MET cc_start: 0.6848 (mtp) cc_final: 0.6512 (ttp) REVERT: E 418 ASN cc_start: 0.6839 (m-40) cc_final: 0.6627 (m110) REVERT: E 420 PHE cc_start: 0.7378 (t80) cc_final: 0.7135 (t80) outliers start: 68 outliers final: 21 residues processed: 330 average time/residue: 0.4645 time to fit residues: 170.4974 Evaluate side-chains 312 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP 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 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 171 GLN 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 E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP 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: 1.9990 chunk 97 optimal weight: 0.0070 chunk 121 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN D 219 ASN B 219 ASN E 219 ASN E 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.157192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119414 restraints weight = 15753.265| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.93 r_work: 0.3167 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14470 Z= 0.187 Angle : 0.741 15.307 19675 Z= 0.373 Chirality : 0.046 0.164 2260 Planarity : 0.004 0.040 2430 Dihedral : 5.774 46.071 1880 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.75 % Allowed : 17.89 % Favored : 77.36 % 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: -1.72 (0.20), residues: 1710 helix: -1.14 (0.21), residues: 575 sheet: 0.47 (0.30), residues: 325 loop : -1.80 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.012 0.002 TYR E 144 PHE 0.014 0.001 PHE D 258 TRP 0.025 0.002 TRP E 255 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (14445) covalent geometry : angle 0.71701 / 0.36 (19610) SS BOND : bond 0.00634 / 0.39 ( 10) SS BOND : angle 5.69452 / 3.66 ( 20) hydrogen bonds : bond 0.03901 / 2.58 ( 532) hydrogen bonds : angle 4.68704 / 3.11 ( 1968) link_BETA1-4 : bond 0.00492 / 0.28 ( 10) link_BETA1-4 : angle 1.53778 / 0.96 ( 30) link_NAG-ASN : bond 0.00069 / 0.03 ( 5) link_NAG-ASN : angle 0.34947 / 0.21 ( 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 365 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 0.533 Fit side-chains REVERT: A 75 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7006 (ttm110) REVERT: A 156 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7291 (mmt) REVERT: A 225 CYS cc_start: 0.6806 (t) cc_final: 0.6464 (t) REVERT: A 260 ILE cc_start: 0.4796 (OUTLIER) cc_final: 0.4534 (pt) REVERT: A 292 LYS cc_start: 0.7757 (mttt) cc_final: 0.7454 (mttp) REVERT: A 391 MET cc_start: 0.7012 (mtp) cc_final: 0.6682 (tmm) REVERT: A 420 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: D 75 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7090 (ttm110) REVERT: D 206 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7732 (mtmm) REVERT: D 207 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7469 (tp30) REVERT: D 212 ARG cc_start: 0.7087 (ptp-110) cc_final: 0.6834 (ptp-170) REVERT: D 225 CYS cc_start: 0.6966 (t) cc_final: 0.6623 (t) REVERT: D 243 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.5874 (mpt) REVERT: D 391 MET cc_start: 0.6848 (mtp) cc_final: 0.6515 (ttp) REVERT: D 420 PHE cc_start: 0.7294 (t80) cc_final: 0.7004 (t80) REVERT: B 28 GLU cc_start: 0.7728 (tp30) cc_final: 0.6975 (tp30) REVERT: B 97 ASP cc_start: 0.7893 (m-30) cc_final: 0.7295 (t0) REVERT: B 102 ASP cc_start: 0.8292 (t70) cc_final: 0.7942 (t70) REVERT: B 126 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6854 (pm20) REVERT: B 188 GLU cc_start: 0.8507 (mp0) cc_final: 0.8296 (mp0) REVERT: B 207 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7482 (tp30) REVERT: B 210 ASP cc_start: 0.7856 (m-30) cc_final: 0.7490 (m-30) REVERT: B 243 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.5650 (mpt) REVERT: C 28 GLU cc_start: 0.7502 (tp30) cc_final: 0.6895 (tp30) REVERT: C 49 LYS cc_start: 0.8472 (mttt) cc_final: 0.7962 (mmtt) REVERT: C 75 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.6868 (ttm110) REVERT: C 97 ASP cc_start: 0.7684 (m-30) cc_final: 0.7089 (t0) REVERT: C 156 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6424 (mmt) REVERT: C 188 GLU cc_start: 0.8549 (mp0) cc_final: 0.8312 (mp0) REVERT: C 212 ARG cc_start: 0.7262 (ptp-110) cc_final: 0.6946 (ptp-170) REVERT: C 229 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7214 (mmt90) REVERT: C 243 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.5477 (mpt) REVERT: C 391 MET cc_start: 0.4456 (tmm) cc_final: 0.4030 (tmm) REVERT: C 401 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5195 (tmt90) REVERT: C 420 PHE cc_start: 0.7427 (t80) cc_final: 0.7211 (m-80) REVERT: E 75 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.6905 (ttm110) REVERT: E 97 ASP cc_start: 0.7866 (m-30) cc_final: 0.7258 (t0) REVERT: E 130 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7561 (t0) REVERT: E 206 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7639 (mmmm) REVERT: E 207 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7543 (tp30) REVERT: E 229 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7243 (mmt90) REVERT: E 262 MET cc_start: 0.4355 (mpp) cc_final: 0.3888 (mpp) REVERT: E 391 MET cc_start: 0.6849 (mtp) cc_final: 0.6508 (ttp) REVERT: E 420 PHE cc_start: 0.7345 (t80) cc_final: 0.7093 (t80) outliers start: 72 outliers final: 33 residues processed: 325 average time/residue: 0.4601 time to fit residues: 166.7934 Evaluate side-chains 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 260 ILE 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 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 243 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 56 THR 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 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 56 THR Chi-restraints excluded: chain C residue 63 SER 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 171 GLN 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 401 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER 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: 0.5980 chunk 86 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN D 219 ASN B 219 ASN B 282 GLN E 219 ASN E 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122669 restraints weight = 15479.005| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.11 r_work: 0.3198 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14470 Z= 0.127 Angle : 0.681 9.365 19675 Z= 0.341 Chirality : 0.044 0.156 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.715 47.871 1880 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.16 % Allowed : 18.94 % Favored : 76.90 % 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: -1.40 (0.20), residues: 1710 helix: -0.88 (0.21), residues: 580 sheet: 0.22 (0.29), residues: 365 loop : -1.46 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.014 0.001 TYR A 144 PHE 0.013 0.001 PHE E 414 TRP 0.036 0.001 TRP E 255 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14445) covalent geometry : angle 0.66478 / 0.33 (19610) SS BOND : bond 0.00216 / 0.14 ( 10) SS BOND : angle 4.33444 / 2.68 ( 20) hydrogen bonds : bond 0.03643 / 2.40 ( 532) hydrogen bonds : angle 4.51123 / 2.99 ( 1968) link_BETA1-4 : bond 0.00461 / 0.27 ( 10) link_BETA1-4 : angle 1.52738 / 0.95 ( 30) link_NAG-ASN : bond 0.00146 / 0.08 ( 5) link_NAG-ASN : angle 0.25838 / 0.15 ( 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 346 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 283 time to evaluate : 0.453 Fit side-chains REVERT: A 75 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7128 (ttm110) REVERT: A 185 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7563 (mt-10) REVERT: A 225 CYS cc_start: 0.7308 (t) cc_final: 0.7057 (t) REVERT: A 227 GLU cc_start: 0.8398 (pt0) cc_final: 0.8154 (tt0) REVERT: A 292 LYS cc_start: 0.7808 (mttt) cc_final: 0.7494 (mttp) REVERT: A 391 MET cc_start: 0.6900 (mtp) cc_final: 0.6598 (tmm) REVERT: A 420 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: D 75 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7229 (ttm110) REVERT: D 130 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7471 (t0) REVERT: D 206 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7840 (mttt) REVERT: D 212 ARG cc_start: 0.7204 (ptp-110) cc_final: 0.6937 (ptp-170) REVERT: D 225 CYS cc_start: 0.7201 (t) cc_final: 0.6941 (t) REVERT: D 243 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6011 (mpt) REVERT: D 391 MET cc_start: 0.6778 (mtp) cc_final: 0.6543 (ttp) REVERT: D 420 PHE cc_start: 0.7380 (t80) cc_final: 0.7088 (t80) REVERT: B 28 GLU cc_start: 0.7673 (tp30) cc_final: 0.6957 (tp30) REVERT: B 97 ASP cc_start: 0.7882 (m-30) cc_final: 0.7334 (t0) REVERT: B 126 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6798 (pm20) REVERT: B 207 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7528 (tp30) REVERT: B 210 ASP cc_start: 0.7923 (m-30) cc_final: 0.7587 (m-30) REVERT: B 229 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7717 (mtp85) REVERT: B 243 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.5674 (mpt) REVERT: C 49 LYS cc_start: 0.8520 (mttt) cc_final: 0.7977 (mmtt) REVERT: C 75 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.6987 (ttm110) REVERT: C 97 ASP cc_start: 0.7711 (m-30) cc_final: 0.7126 (t0) REVERT: C 156 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6310 (mmt) REVERT: C 188 GLU cc_start: 0.8568 (mp0) cc_final: 0.8328 (mp0) REVERT: C 243 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5538 (mpt) REVERT: C 262 MET cc_start: 0.4124 (mpp) cc_final: 0.3914 (mpp) REVERT: C 391 MET cc_start: 0.4345 (tmm) cc_final: 0.3935 (tmm) REVERT: C 420 PHE cc_start: 0.7420 (t80) cc_final: 0.7220 (m-80) REVERT: E 75 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7035 (ttm110) REVERT: E 97 ASP cc_start: 0.7909 (m-30) cc_final: 0.7363 (t0) REVERT: E 130 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 206 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7765 (mmmm) REVERT: E 229 ARG cc_start: 0.7788 (mmt90) cc_final: 0.7340 (mmt90) REVERT: E 262 MET cc_start: 0.4355 (mpp) cc_final: 0.3923 (mpp) REVERT: E 391 MET cc_start: 0.6868 (mtp) cc_final: 0.6555 (ttp) REVERT: E 420 PHE cc_start: 0.7235 (t80) cc_final: 0.7023 (t80) outliers start: 63 outliers final: 25 residues processed: 313 average time/residue: 0.4538 time to fit residues: 158.0814 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE 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 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 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 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 171 GLN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 104 SER 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 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN D 219 ASN B 219 ASN E 219 ASN E 282 GLN E 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.160492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121430 restraints weight = 15485.496| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.11 r_work: 0.3227 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14470 Z= 0.145 Angle : 0.690 9.225 19675 Z= 0.347 Chirality : 0.045 0.165 2260 Planarity : 0.004 0.043 2430 Dihedral : 5.701 47.689 1880 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.83 % Allowed : 19.74 % Favored : 76.44 % 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: -1.21 (0.20), residues: 1710 helix: -0.60 (0.22), residues: 580 sheet: 0.20 (0.29), residues: 370 loop : -1.40 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.014 0.002 TYR A 144 PHE 0.013 0.001 PHE A 124 TRP 0.040 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (14445) covalent geometry : angle 0.67483 / 0.34 (19610) SS BOND : bond 0.00444 / 0.30 ( 10) SS BOND : angle 4.20200 / 2.59 ( 20) hydrogen bonds : bond 0.03642 / 2.41 ( 532) hydrogen bonds : angle 4.47925 / 2.97 ( 1968) link_BETA1-4 : bond 0.00451 / 0.26 ( 10) link_BETA1-4 : angle 1.52300 / 0.95 ( 30) link_NAG-ASN : bond 0.00082 / 0.04 ( 5) link_NAG-ASN : angle 0.34235 / 0.20 ( 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 344 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 0.407 Fit side-chains REVERT: A 75 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7127 (ttm110) REVERT: A 96 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7529 (t0) REVERT: A 185 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7553 (mt-10) REVERT: A 227 GLU cc_start: 0.8413 (pt0) cc_final: 0.8185 (tt0) REVERT: A 292 LYS cc_start: 0.7899 (mttt) cc_final: 0.7568 (mttp) REVERT: A 391 MET cc_start: 0.6908 (mtp) cc_final: 0.6635 (tmm) REVERT: A 420 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: D 75 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7215 (ttm110) REVERT: D 130 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7486 (t0) REVERT: D 212 ARG cc_start: 0.7225 (ptp-110) cc_final: 0.6932 (ptp-170) REVERT: D 225 CYS cc_start: 0.7134 (t) cc_final: 0.6915 (t) REVERT: D 229 ARG cc_start: 0.7905 (mpt-90) cc_final: 0.7658 (mmm-85) REVERT: D 243 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6099 (mpt) REVERT: D 391 MET cc_start: 0.6803 (mtp) cc_final: 0.6537 (tmm) REVERT: D 420 PHE cc_start: 0.7413 (t80) cc_final: 0.7108 (t80) REVERT: B 28 GLU cc_start: 0.7740 (tp30) cc_final: 0.6998 (tp30) REVERT: B 97 ASP cc_start: 0.7856 (m-30) cc_final: 0.7368 (t0) REVERT: B 126 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6891 (pm20) REVERT: B 179 MET cc_start: 0.8212 (tpt) cc_final: 0.7870 (tpt) REVERT: B 207 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7556 (tp30) REVERT: B 210 ASP cc_start: 0.7926 (m-30) cc_final: 0.7623 (m-30) REVERT: C 49 LYS cc_start: 0.8557 (mttt) cc_final: 0.8036 (mmtt) REVERT: C 58 ASN cc_start: 0.7917 (p0) cc_final: 0.7685 (p0) REVERT: C 75 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.6967 (ttm110) REVERT: C 97 ASP cc_start: 0.7725 (m-30) cc_final: 0.7148 (t0) REVERT: C 156 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.6384 (mmt) REVERT: C 188 GLU cc_start: 0.8574 (mp0) cc_final: 0.8334 (mp0) REVERT: C 243 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.5545 (mpt) REVERT: C 391 MET cc_start: 0.4266 (tmm) cc_final: 0.3838 (tmm) REVERT: C 420 PHE cc_start: 0.7438 (t80) cc_final: 0.7211 (m-80) REVERT: E 75 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7015 (ttm110) REVERT: E 105 MET cc_start: 0.6599 (mmp) cc_final: 0.6189 (mtm) REVERT: E 130 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7604 (t0) REVERT: E 206 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7782 (mmmm) REVERT: E 229 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7415 (mmt90) REVERT: E 262 MET cc_start: 0.4438 (mpp) cc_final: 0.4018 (mpp) REVERT: E 391 MET cc_start: 0.6863 (mtp) cc_final: 0.6568 (ttp) REVERT: E 420 PHE cc_start: 0.7177 (t80) cc_final: 0.6970 (t80) outliers start: 58 outliers final: 32 residues processed: 311 average time/residue: 0.4263 time to fit residues: 149.2106 Evaluate side-chains 312 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 96 ASP 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 63 SER 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 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 ASP 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 167 THR Chi-restraints excluded: chain B residue 171 GLN 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 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 170 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 104 SER 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 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN D 219 ASN B 219 ASN B 282 GLN E 219 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124424 restraints weight = 15574.671| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.23 r_work: 0.3203 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14470 Z= 0.147 Angle : 0.689 10.134 19675 Z= 0.345 Chirality : 0.045 0.163 2260 Planarity : 0.004 0.036 2430 Dihedral : 5.688 48.181 1880 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.56 % Allowed : 20.59 % Favored : 75.84 % 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: -1.08 (0.20), residues: 1710 helix: -0.41 (0.22), residues: 580 sheet: 0.19 (0.28), residues: 370 loop : -1.36 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.013 0.002 TYR A 144 PHE 0.013 0.001 PHE E 414 TRP 0.031 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14445) covalent geometry : angle 0.67529 / 0.34 (19610) SS BOND : bond 0.00312 / 0.19 ( 10) SS BOND : angle 4.02751 / 2.40 ( 20) hydrogen bonds : bond 0.03620 / 2.40 ( 532) hydrogen bonds : angle 4.45166 / 2.95 ( 1968) link_BETA1-4 : bond 0.00442 / 0.26 ( 10) link_BETA1-4 : angle 1.51733 / 0.94 ( 30) link_NAG-ASN : bond 0.00097 / 0.05 ( 5) link_NAG-ASN : angle 0.33293 / 0.19 ( 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 335 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.534 Fit side-chains REVERT: A 75 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7304 (ttm110) REVERT: A 96 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7508 (t0) REVERT: A 227 GLU cc_start: 0.8548 (pt0) cc_final: 0.8337 (tt0) REVERT: A 292 LYS cc_start: 0.8075 (mttt) cc_final: 0.7735 (mttp) REVERT: A 391 MET cc_start: 0.6938 (mtp) cc_final: 0.6682 (tmm) REVERT: A 420 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: D 75 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7405 (ttm110) REVERT: D 130 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7607 (t0) REVERT: D 179 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7983 (tpt) REVERT: D 212 ARG cc_start: 0.7506 (ptp-110) cc_final: 0.7107 (ptp-170) REVERT: D 229 ARG cc_start: 0.8103 (mpt-90) cc_final: 0.7894 (mmm-85) REVERT: D 243 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6229 (mpt) REVERT: D 391 MET cc_start: 0.6782 (mtp) cc_final: 0.6514 (tmm) REVERT: D 420 PHE cc_start: 0.7511 (t80) cc_final: 0.7207 (t80) REVERT: B 28 GLU cc_start: 0.7794 (tp30) cc_final: 0.7069 (tp30) REVERT: B 97 ASP cc_start: 0.7883 (m-30) cc_final: 0.7399 (t0) REVERT: B 126 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7022 (pm20) REVERT: B 179 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7979 (tpt) REVERT: B 207 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7622 (tp30) REVERT: B 210 ASP cc_start: 0.8055 (m-30) cc_final: 0.7757 (m-30) REVERT: B 229 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7967 (mtp85) REVERT: C 28 GLU cc_start: 0.7585 (tp30) cc_final: 0.6952 (tp30) REVERT: C 49 LYS cc_start: 0.8655 (mttt) cc_final: 0.8160 (mmtt) REVERT: C 75 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7158 (ttm110) REVERT: C 97 ASP cc_start: 0.7839 (m-30) cc_final: 0.7286 (t0) REVERT: C 188 GLU cc_start: 0.8568 (mp0) cc_final: 0.8338 (mp0) REVERT: C 243 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.5738 (mpt) REVERT: C 420 PHE cc_start: 0.7430 (t80) cc_final: 0.7203 (m-80) REVERT: E 75 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7200 (ttm110) REVERT: E 97 ASP cc_start: 0.7974 (m-30) cc_final: 0.7415 (t0) REVERT: E 105 MET cc_start: 0.6675 (mmp) cc_final: 0.6296 (mtm) REVERT: E 130 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7689 (t0) REVERT: E 206 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7977 (mmmm) REVERT: E 229 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7592 (mmt90) REVERT: E 262 MET cc_start: 0.4514 (mpp) cc_final: 0.4091 (mpp) REVERT: E 391 MET cc_start: 0.6881 (mtp) cc_final: 0.6625 (tmm) REVERT: E 420 PHE cc_start: 0.7237 (t80) cc_final: 0.7023 (t80) outliers start: 54 outliers final: 32 residues processed: 302 average time/residue: 0.4716 time to fit residues: 158.6205 Evaluate side-chains 321 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 96 ASP 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 179 MET Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 ASP 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 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 63 SER 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 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER 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 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 91 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN D 219 ASN B 219 ASN B 282 GLN C 282 GLN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123393 restraints weight = 15534.783| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.09 r_work: 0.3245 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14470 Z= 0.124 Angle : 0.689 11.702 19675 Z= 0.341 Chirality : 0.044 0.159 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.611 49.110 1880 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.84 % Allowed : 22.05 % Favored : 75.12 % 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: -0.91 (0.20), residues: 1710 helix: -0.16 (0.22), residues: 580 sheet: 0.22 (0.28), residues: 370 loop : -1.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.012 0.001 TYR A 144 PHE 0.016 0.001 PHE E 414 TRP 0.030 0.001 TRP E 255 HIS 0.002 0.000 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14445) covalent geometry : angle 0.67658 / 0.34 (19610) SS BOND : bond 0.00329 / 0.18 ( 10) SS BOND : angle 3.83755 / 2.26 ( 20) hydrogen bonds : bond 0.03499 / 2.32 ( 532) hydrogen bonds : angle 4.37158 / 2.90 ( 1968) link_BETA1-4 : bond 0.00448 / 0.26 ( 10) link_BETA1-4 : angle 1.52124 / 0.94 ( 30) link_NAG-ASN : bond 0.00126 / 0.07 ( 5) link_NAG-ASN : angle 0.28098 / 0.16 ( 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 324 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.539 Fit side-chains REVERT: A 62 ASN cc_start: 0.8702 (t0) cc_final: 0.8502 (t0) REVERT: A 75 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7113 (ttm110) REVERT: A 108 SER cc_start: 0.8627 (t) cc_final: 0.8385 (t) REVERT: A 163 MET cc_start: 0.7960 (mtm) cc_final: 0.7739 (mpp) REVERT: A 227 GLU cc_start: 0.8327 (pt0) cc_final: 0.8096 (tt0) REVERT: A 292 LYS cc_start: 0.7853 (mttt) cc_final: 0.7537 (mttp) REVERT: A 391 MET cc_start: 0.6979 (mtp) cc_final: 0.6681 (tmm) REVERT: A 420 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: D 75 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7183 (ttm110) REVERT: D 130 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7404 (t0) REVERT: D 212 ARG cc_start: 0.7271 (ptp-110) cc_final: 0.6882 (ptp-170) REVERT: D 229 ARG cc_start: 0.7880 (mpt-90) cc_final: 0.7662 (mmm-85) REVERT: D 243 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6007 (mpt) REVERT: D 391 MET cc_start: 0.6756 (mtp) cc_final: 0.6465 (tmm) REVERT: D 420 PHE cc_start: 0.7417 (t80) cc_final: 0.7100 (t80) REVERT: B 28 GLU cc_start: 0.7758 (tp30) cc_final: 0.7026 (tp30) REVERT: B 97 ASP cc_start: 0.7765 (m-30) cc_final: 0.7243 (t0) REVERT: B 126 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6824 (pm20) REVERT: B 207 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7534 (tp30) REVERT: B 210 ASP cc_start: 0.7937 (m-30) cc_final: 0.7641 (m-30) REVERT: B 229 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7593 (mtp85) REVERT: C 49 LYS cc_start: 0.8590 (mttt) cc_final: 0.8070 (mmtt) REVERT: C 75 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.6949 (ttm110) REVERT: C 97 ASP cc_start: 0.7688 (m-30) cc_final: 0.7113 (t0) REVERT: C 105 MET cc_start: 0.6498 (mmp) cc_final: 0.6258 (mtm) REVERT: C 188 GLU cc_start: 0.8511 (mp0) cc_final: 0.8261 (mp0) REVERT: C 420 PHE cc_start: 0.7345 (t80) cc_final: 0.7097 (m-80) REVERT: E 75 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.6982 (ttm110) REVERT: E 97 ASP cc_start: 0.7784 (m-30) cc_final: 0.7282 (t0) REVERT: E 105 MET cc_start: 0.6522 (mmp) cc_final: 0.6119 (mtm) REVERT: E 130 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7570 (t0) REVERT: E 206 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7785 (mmmm) REVERT: E 229 ARG cc_start: 0.7667 (mmt90) cc_final: 0.7388 (mmt90) REVERT: E 262 MET cc_start: 0.4300 (mpp) cc_final: 0.3860 (mpp) REVERT: E 391 MET cc_start: 0.6807 (mtp) cc_final: 0.6539 (ttp) REVERT: E 420 PHE cc_start: 0.7032 (t80) cc_final: 0.6817 (t80) outliers start: 43 outliers final: 27 residues processed: 296 average time/residue: 0.4610 time to fit residues: 151.9894 Evaluate side-chains 301 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 63 SER 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 165 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 ASP 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 165 VAL 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 C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain E residue 63 SER 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 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 134 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 219 ASN C 171 GLN E 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123836 restraints weight = 15417.900| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.08 r_work: 0.3254 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14470 Z= 0.121 Angle : 0.684 11.033 19675 Z= 0.338 Chirality : 0.044 0.208 2260 Planarity : 0.004 0.031 2430 Dihedral : 5.532 47.354 1880 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.64 % Allowed : 22.44 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -0.78 (0.20), residues: 1710 helix: -0.00 (0.22), residues: 580 sheet: 0.35 (0.28), residues: 365 loop : -1.31 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.014 0.001 TYR E 317 PHE 0.016 0.001 PHE E 414 TRP 0.029 0.001 TRP E 255 HIS 0.002 0.000 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14445) covalent geometry : angle 0.67210 / 0.33 (19610) SS BOND : bond 0.00322 / 0.19 ( 10) SS BOND : angle 3.79892 / 2.21 ( 20) hydrogen bonds : bond 0.03431 / 2.27 ( 532) hydrogen bonds : angle 4.29722 / 2.86 ( 1968) link_BETA1-4 : bond 0.00453 / 0.26 ( 10) link_BETA1-4 : angle 1.51998 / 0.94 ( 30) link_NAG-ASN : bond 0.00112 / 0.06 ( 5) link_NAG-ASN : angle 0.29313 / 0.17 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4181.74 seconds wall clock time: 72 minutes 2.75 seconds (4322.75 seconds total)