Starting phenix.real_space_refine on Thu Jun 4 16:37:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm2_20384/06_2026/6pm2_20384.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.062 sd= 2.734 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 105 5.16 5 C 9190 2.51 5 N 2265 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14125 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14125 At special positions: 0 Unit cell: (106.167, 104.521, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2565 8.00 N 2265 7.00 C 9190 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 640.8 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 41.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.555A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.021A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.536A 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 102 through 109 removed outlier: 3.584A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.978A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 266 through 286 removed outlier: 3.915A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 4.092A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 428 removed outlier: 3.929A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.082A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.536A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.034A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.142A 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 removed outlier: 3.539A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.569A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 255 removed outlier: 4.049A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 266 through 286 removed outlier: 3.812A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 4.084A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 428 removed outlier: 3.934A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.087A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.538A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.013A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 4.142A 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: 3.539A 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 102 through 109 removed outlier: 3.560A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 255 removed outlier: 4.063A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 Processing helix chain 'C' and resid 266 through 286 removed outlier: 3.790A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 4.055A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 428 removed outlier: 3.961A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.067A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.516A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.028A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 4.129A 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: 3.563A 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 102 through 109 removed outlier: 3.598A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 255 removed outlier: 4.011A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 266 through 286 removed outlier: 3.816A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 4.108A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 428 removed outlier: 3.935A pdb=" N LYS D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.084A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 428 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.579A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.023A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 4.141A 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: 3.571A 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 102 through 109 removed outlier: 3.574A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.992A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'E' and resid 266 through 286 removed outlier: 3.824A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 325 removed outlier: 4.120A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 428 removed outlier: 3.901A pdb=" N LYS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.043A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 428 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.652A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.492A 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: 6.362A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.672A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.347A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.750A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.353A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.703A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.310A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.686A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 6.369A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.162A 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 217 678 hydrogen bonds defined for protein. 1965 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: 2.42 Time building geometry restraints manager: 1.46 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: 4328 1.34 - 1.47: 3624 1.47 - 1.59: 6343 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14470 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 14465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19112 2.41 - 4.81: 408 4.81 - 7.22: 84 7.22 - 9.63: 41 9.63 - 12.03: 5 Bond angle restraints: 19650 Sorted by residual: angle pdb=" N VAL E 276 " pdb=" CA VAL E 276 " pdb=" C VAL E 276 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.09 -9.55 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.09 -9.55 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.47e+01 ... (remaining 19645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 8336 15.45 - 30.91: 368 30.91 - 46.36: 66 46.36 - 61.82: 43 61.82 - 77.27: 17 Dihedral angle restraints: 8830 sinusoidal: 3715 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual 180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN D 160 " pdb=" C ASN D 160 " pdb=" N PHE D 161 " pdb=" CA PHE D 161 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN B 160 " pdb=" C ASN B 160 " pdb=" N PHE B 161 " pdb=" CA PHE B 161 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1579 0.050 - 0.100: 528 0.100 - 0.150: 124 0.150 - 0.200: 19 0.200 - 0.250: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.56e+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 -2.52 0.25 2.00e-01 2.50e+01 1.56e+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 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO D 411 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO B 411 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 411 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.039 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4486 2.84 - 3.36: 12184 3.36 - 3.87: 22623 3.87 - 4.39: 26476 4.39 - 4.90: 45259 Nonbonded interactions: 111028 Sorted by model distance: nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.335 3.040 nonbonded pdb=" OG SER D 145 " pdb=" O3 TAU D 504 " model vdw 2.336 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.336 3.040 nonbonded pdb=" OG SER C 145 " pdb=" O3 TAU C 504 " model vdw 2.337 3.040 ... (remaining 111023 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.310 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:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.004 0.041 14495 Z= 0.206 Angle : 0.955 12.032 19715 Z= 0.477 Chirality : 0.054 0.250 2260 Planarity : 0.007 0.071 2430 Dihedral : 11.033 77.271 5480 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -5.02 (0.15), residues: 1710 helix: -4.83 (0.07), residues: 530 sheet: -2.31 (0.22), residues: 385 loop : -2.63 (0.17), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 81 TYR 0.014 0.002 TYR A 74 PHE 0.019 0.002 PHE C 115 TRP 0.018 0.002 TRP E 110 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (14470) covalent geometry : angle 0.95084 / 0.48 (19650) SS BOND : bond 0.00528 / 0.29 ( 10) SS BOND : angle 2.72224 / 1.64 ( 20) hydrogen bonds : bond 0.28192 / 18.20 ( 533) hydrogen bonds : angle 9.62962 / 6.71 ( 1965) link_BETA1-4 : bond 0.00651 / 0.37 ( 10) link_BETA1-4 : angle 1.41359 / 0.91 ( 30) link_NAG-ASN : bond 0.00062 / 0.04 ( 5) link_NAG-ASN : angle 1.01055 / 0.56 ( 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 455 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8748 (mtm180) REVERT: A 210 ASP cc_start: 0.7969 (m-30) cc_final: 0.7671 (m-30) REVERT: A 233 GLU cc_start: 0.7482 (tt0) cc_final: 0.7194 (mt-10) REVERT: A 398 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6117 (tpp-160) REVERT: A 416 ILE cc_start: 0.8871 (tp) cc_final: 0.8621 (tp) REVERT: B 43 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8532 (mtm180) REVERT: B 75 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7481 (ttp-110) REVERT: B 233 GLU cc_start: 0.7296 (tt0) cc_final: 0.7000 (mt-10) REVERT: B 398 ARG cc_start: 0.6762 (ttm110) cc_final: 0.5935 (tpp-160) REVERT: C 41 ASP cc_start: 0.8764 (t0) cc_final: 0.8523 (t0) REVERT: C 43 ARG cc_start: 0.9060 (mtm-85) cc_final: 0.8624 (mtm180) REVERT: C 75 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: C 210 ASP cc_start: 0.8039 (m-30) cc_final: 0.7750 (m-30) REVERT: C 233 GLU cc_start: 0.7366 (tt0) cc_final: 0.7137 (mt-10) REVERT: C 398 ARG cc_start: 0.6726 (ttm110) cc_final: 0.5936 (tpp-160) REVERT: C 416 ILE cc_start: 0.8757 (tp) cc_final: 0.8540 (tp) REVERT: D 75 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7229 (ttm-80) REVERT: D 81 ARG cc_start: 0.7947 (mpt-90) cc_final: 0.6294 (mpp-170) REVERT: D 113 ASP cc_start: 0.8476 (p0) cc_final: 0.8215 (p0) REVERT: D 210 ASP cc_start: 0.8068 (m-30) cc_final: 0.7672 (m-30) REVERT: D 233 GLU cc_start: 0.7441 (tt0) cc_final: 0.7100 (mt-10) REVERT: D 398 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6242 (tpp-160) REVERT: D 400 LYS cc_start: 0.6606 (tmtp) cc_final: 0.6339 (tmmt) REVERT: D 416 ILE cc_start: 0.8848 (tp) cc_final: 0.8498 (tp) REVERT: E 210 ASP cc_start: 0.8092 (m-30) cc_final: 0.7656 (m-30) REVERT: E 233 GLU cc_start: 0.7281 (tt0) cc_final: 0.7038 (mt-10) REVERT: E 398 ARG cc_start: 0.6714 (ttm110) cc_final: 0.6061 (tpp-160) REVERT: E 416 ILE cc_start: 0.8833 (tp) cc_final: 0.8624 (tp) outliers start: 0 outliers final: 2 residues processed: 455 average time/residue: 0.5209 time to fit residues: 260.6314 Evaluate side-chains 282 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain C residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 141 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 131 ASN B 180 ASN B 231 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 131 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 131 ASN D 141 ASN D 180 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112682 restraints weight = 17529.276| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.11 r_work: 0.3187 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14495 Z= 0.172 Angle : 0.718 7.412 19715 Z= 0.370 Chirality : 0.047 0.153 2260 Planarity : 0.005 0.042 2430 Dihedral : 8.349 43.260 2194 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.41 % Allowed : 13.03 % Favored : 82.57 % 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: -3.61 (0.16), residues: 1710 helix: -2.90 (0.16), residues: 575 sheet: -1.16 (0.26), residues: 340 loop : -2.49 (0.17), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 229 TYR 0.027 0.002 TYR B 238 PHE 0.015 0.002 PHE C 414 TRP 0.011 0.002 TRP D 84 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (14470) covalent geometry : angle 0.70975 / 0.37 (19650) SS BOND : bond 0.00555 / 0.31 ( 10) SS BOND : angle 1.61286 / 0.95 ( 20) hydrogen bonds : bond 0.05161 / 3.43 ( 533) hydrogen bonds : angle 5.48125 / 3.76 ( 1965) link_BETA1-4 : bond 0.00279 / 0.15 ( 10) link_BETA1-4 : angle 2.66811 / 1.72 ( 30) link_NAG-ASN : bond 0.00169 / 0.10 ( 5) link_NAG-ASN : angle 0.62691 / 0.40 ( 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 356 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8125 (tt0) cc_final: 0.7385 (tm-30) REVERT: A 71 THR cc_start: 0.9244 (p) cc_final: 0.8875 (p) REVERT: A 72 MET cc_start: 0.9084 (mtt) cc_final: 0.8716 (mtt) REVERT: A 126 GLU cc_start: 0.7530 (pm20) cc_final: 0.7156 (mt-10) REVERT: A 227 GLU cc_start: 0.8763 (pt0) cc_final: 0.8475 (pt0) REVERT: A 233 GLU cc_start: 0.7560 (tt0) cc_final: 0.7064 (mt-10) REVERT: A 391 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3646 (tmm) REVERT: A 398 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6479 (tpp-160) REVERT: B 28 GLU cc_start: 0.8181 (tp30) cc_final: 0.7677 (tm-30) REVERT: B 126 GLU cc_start: 0.7639 (pm20) cc_final: 0.7253 (mt-10) REVERT: B 398 ARG cc_start: 0.6993 (ttm110) cc_final: 0.6286 (tpp-160) REVERT: C 28 GLU cc_start: 0.8208 (tp30) cc_final: 0.7782 (tm-30) REVERT: D 28 GLU cc_start: 0.8150 (tt0) cc_final: 0.7690 (tm-30) REVERT: D 75 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: D 113 ASP cc_start: 0.8659 (p0) cc_final: 0.8415 (p0) REVERT: D 126 GLU cc_start: 0.7652 (pm20) cc_final: 0.7269 (mt-10) REVERT: D 206 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8145 (mttp) REVERT: D 398 ARG cc_start: 0.7293 (ttm110) cc_final: 0.6516 (tpp-160) REVERT: D 400 LYS cc_start: 0.6585 (tmtp) cc_final: 0.6268 (tmmt) REVERT: E 49 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: E 126 GLU cc_start: 0.7544 (pm20) cc_final: 0.7177 (mt-10) REVERT: E 210 ASP cc_start: 0.8197 (m-30) cc_final: 0.7738 (m-30) REVERT: E 233 GLU cc_start: 0.7591 (tt0) cc_final: 0.7088 (mt-10) REVERT: E 398 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6469 (tpp-160) outliers start: 67 outliers final: 25 residues processed: 330 average time/residue: 0.5522 time to fit residues: 199.6590 Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 404 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.0020 chunk 102 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 158 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 141 ASN B 235 GLN C 85 ASN C 141 ASN C 231 HIS D 62 ASN D 180 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 141 ASN E 261 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106859 restraints weight = 17831.762| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.06 r_work: 0.3060 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14495 Z= 0.217 Angle : 0.729 10.648 19715 Z= 0.365 Chirality : 0.047 0.150 2260 Planarity : 0.004 0.040 2430 Dihedral : 6.847 32.181 2192 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.66 % Allowed : 14.21 % Favored : 80.13 % 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: -2.67 (0.18), residues: 1710 helix: -1.81 (0.20), residues: 545 sheet: -0.67 (0.27), residues: 345 loop : -2.20 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 229 TYR 0.019 0.002 TYR C 238 PHE 0.015 0.002 PHE D 124 TRP 0.012 0.002 TRP B 302 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (14470) covalent geometry : angle 0.72151 / 0.36 (19650) SS BOND : bond 0.00635 / 0.36 ( 10) SS BOND : angle 1.85025 / 1.10 ( 20) hydrogen bonds : bond 0.04455 / 2.96 ( 533) hydrogen bonds : angle 4.86070 / 3.34 ( 1965) link_BETA1-4 : bond 0.00598 / 0.31 ( 10) link_BETA1-4 : angle 2.28769 / 1.57 ( 30) link_NAG-ASN : bond 0.00088 / 0.05 ( 5) link_NAG-ASN : angle 0.83890 / 0.55 ( 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 365 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 279 time to evaluate : 0.540 Fit side-chains REVERT: A 24 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8053 (tpt) REVERT: A 71 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 72 MET cc_start: 0.9143 (mtt) cc_final: 0.8824 (mtt) REVERT: A 126 GLU cc_start: 0.7578 (pm20) cc_final: 0.7187 (mt-10) REVERT: A 233 GLU cc_start: 0.7661 (tt0) cc_final: 0.7159 (mt-10) REVERT: A 391 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.4310 (tmt) REVERT: A 398 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6574 (tpp-160) REVERT: A 401 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.5031 (tpt-90) REVERT: B 28 GLU cc_start: 0.8164 (tp30) cc_final: 0.7769 (tm-30) REVERT: B 97 ASP cc_start: 0.8306 (m-30) cc_final: 0.7667 (t0) REVERT: B 126 GLU cc_start: 0.7619 (pm20) cc_final: 0.7320 (mm-30) REVERT: B 233 GLU cc_start: 0.7713 (tt0) cc_final: 0.7189 (mt-10) REVERT: B 236 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7050 (tmm) REVERT: B 398 ARG cc_start: 0.7117 (ttm110) cc_final: 0.6287 (tpp-160) REVERT: C 28 GLU cc_start: 0.8217 (tp30) cc_final: 0.7751 (tm-30) REVERT: C 49 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8445 (mtmt) REVERT: C 126 GLU cc_start: 0.7489 (pm20) cc_final: 0.7255 (mm-30) REVERT: C 189 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8598 (mtpt) REVERT: C 206 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8137 (mttm) REVERT: C 391 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5119 (tmm) REVERT: D 28 GLU cc_start: 0.8134 (tt0) cc_final: 0.7662 (tm-30) REVERT: D 75 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: D 113 ASP cc_start: 0.8753 (p0) cc_final: 0.8371 (p0) REVERT: D 126 GLU cc_start: 0.7648 (pm20) cc_final: 0.7263 (mt-10) REVERT: D 206 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8527 (mtpm) REVERT: D 227 GLU cc_start: 0.8781 (pt0) cc_final: 0.8332 (pt0) REVERT: D 233 GLU cc_start: 0.7569 (tt0) cc_final: 0.7090 (mt-10) REVERT: D 235 GLN cc_start: 0.8531 (mm110) cc_final: 0.8107 (mt0) REVERT: D 236 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7540 (tmm) REVERT: D 395 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: D 398 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6587 (tpp-160) REVERT: D 400 LYS cc_start: 0.6617 (tmtp) cc_final: 0.6217 (tmmt) REVERT: E 24 MET cc_start: 0.8257 (tpt) cc_final: 0.7887 (tpt) REVERT: E 49 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8450 (mtmt) REVERT: E 126 GLU cc_start: 0.7512 (pm20) cc_final: 0.7175 (mt-10) REVERT: E 233 GLU cc_start: 0.7696 (tt0) cc_final: 0.7163 (mt-10) REVERT: E 398 ARG cc_start: 0.7393 (ttm110) cc_final: 0.6592 (tpp-160) outliers start: 86 outliers final: 39 residues processed: 321 average time/residue: 0.5528 time to fit residues: 194.5806 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 395 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 180 ASN A 261 ASN B 261 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 261 ASN D 62 ASN D 180 ASN D 261 ASN E 58 ASN E 418 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110599 restraints weight = 17289.091| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.27 r_work: 0.3062 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14495 Z= 0.135 Angle : 0.641 7.488 19715 Z= 0.323 Chirality : 0.045 0.150 2260 Planarity : 0.004 0.039 2430 Dihedral : 5.572 21.439 2192 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.08 % Allowed : 17.43 % Favored : 78.49 % 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: -2.15 (0.19), residues: 1710 helix: -1.18 (0.21), residues: 560 sheet: -0.33 (0.28), residues: 345 loop : -2.08 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 229 TYR 0.024 0.002 TYR D 238 PHE 0.012 0.001 PHE A 258 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14470) covalent geometry : angle 0.63512 / 0.32 (19650) SS BOND : bond 0.00487 / 0.27 ( 10) SS BOND : angle 1.49948 / 0.87 ( 20) hydrogen bonds : bond 0.03704 / 2.47 ( 533) hydrogen bonds : angle 4.33687 / 2.98 ( 1965) link_BETA1-4 : bond 0.00441 / 0.25 ( 10) link_BETA1-4 : angle 1.95357 / 1.32 ( 30) link_NAG-ASN : bond 0.00034 / 0.02 ( 5) link_NAG-ASN : angle 0.68594 / 0.44 ( 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 339 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7555 (tm-30) REVERT: A 97 ASP cc_start: 0.8042 (m-30) cc_final: 0.7187 (t0) REVERT: A 126 GLU cc_start: 0.7389 (pm20) cc_final: 0.6881 (mt-10) REVERT: A 233 GLU cc_start: 0.7462 (tt0) cc_final: 0.6983 (mt-10) REVERT: A 398 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6391 (tpp-160) REVERT: B 28 GLU cc_start: 0.8160 (tp30) cc_final: 0.7723 (tm-30) REVERT: B 97 ASP cc_start: 0.8333 (m-30) cc_final: 0.7645 (t0) REVERT: B 126 GLU cc_start: 0.7487 (pm20) cc_final: 0.7037 (mm-30) REVERT: B 398 ARG cc_start: 0.6919 (ttm110) cc_final: 0.6016 (tpp-160) REVERT: C 28 GLU cc_start: 0.8140 (tp30) cc_final: 0.7677 (tm-30) REVERT: C 49 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8361 (mtmt) REVERT: C 97 ASP cc_start: 0.8149 (m-30) cc_final: 0.7438 (t0) REVERT: C 180 ASN cc_start: 0.8551 (p0) cc_final: 0.8351 (p0) REVERT: C 189 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: C 206 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7901 (mttm) REVERT: C 227 GLU cc_start: 0.8698 (pt0) cc_final: 0.8126 (pt0) REVERT: C 391 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4971 (tmm) REVERT: D 28 GLU cc_start: 0.8003 (tt0) cc_final: 0.7590 (tm-30) REVERT: D 75 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7649 (ttm-80) REVERT: D 97 ASP cc_start: 0.8069 (m-30) cc_final: 0.7281 (t0) REVERT: D 113 ASP cc_start: 0.8742 (p0) cc_final: 0.8349 (p0) REVERT: D 126 GLU cc_start: 0.7493 (pm20) cc_final: 0.6943 (mt-10) REVERT: D 206 LYS cc_start: 0.8558 (mtpt) cc_final: 0.7977 (mttp) REVERT: D 207 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: D 235 GLN cc_start: 0.8537 (mm110) cc_final: 0.8091 (mt0) REVERT: D 395 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6567 (m-10) REVERT: D 398 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6536 (tpp-160) REVERT: D 400 LYS cc_start: 0.6406 (tmtp) cc_final: 0.5980 (tmmt) REVERT: E 28 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7672 (tm-30) REVERT: E 49 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8359 (mtmt) REVERT: E 97 ASP cc_start: 0.8224 (m-30) cc_final: 0.7442 (t0) REVERT: E 126 GLU cc_start: 0.7425 (pm20) cc_final: 0.6918 (mt-10) REVERT: E 179 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (mmt) REVERT: E 233 GLU cc_start: 0.7419 (tt0) cc_final: 0.6877 (mt-10) REVERT: E 236 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7282 (tmm) REVERT: E 395 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: E 398 ARG cc_start: 0.7233 (ttm110) cc_final: 0.6516 (tpp-160) outliers start: 62 outliers final: 30 residues processed: 302 average time/residue: 0.5473 time to fit residues: 181.2082 Evaluate side-chains 299 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 395 PHE Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 180 ASN B 58 ASN B 62 ASN B 82 GLN B 131 ASN C 58 ASN C 62 ASN D 62 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106664 restraints weight = 17232.306| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.21 r_work: 0.3052 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14495 Z= 0.144 Angle : 0.643 9.265 19715 Z= 0.323 Chirality : 0.045 0.136 2260 Planarity : 0.004 0.038 2430 Dihedral : 4.988 20.572 2192 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.39 % Allowed : 17.11 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.19), residues: 1710 helix: -0.85 (0.22), residues: 555 sheet: -0.22 (0.28), residues: 345 loop : -1.94 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 229 TYR 0.027 0.002 TYR C 238 PHE 0.014 0.001 PHE A 258 TRP 0.010 0.001 TRP C 422 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (14470) covalent geometry : angle 0.63824 / 0.32 (19650) SS BOND : bond 0.00518 / 0.29 ( 10) SS BOND : angle 1.56485 / 0.93 ( 20) hydrogen bonds : bond 0.03545 / 2.37 ( 533) hydrogen bonds : angle 4.19245 / 2.88 ( 1965) link_BETA1-4 : bond 0.00510 / 0.29 ( 10) link_BETA1-4 : angle 1.68273 / 1.12 ( 30) link_NAG-ASN : bond 0.00035 / 0.02 ( 5) link_NAG-ASN : angle 0.70460 / 0.45 ( 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 347 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7528 (tm-30) REVERT: A 36 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8766 (mtpm) REVERT: A 97 ASP cc_start: 0.8086 (m-30) cc_final: 0.7290 (t0) REVERT: A 126 GLU cc_start: 0.7470 (pm20) cc_final: 0.6976 (mt-10) REVERT: A 233 GLU cc_start: 0.7565 (tt0) cc_final: 0.7075 (mt-10) REVERT: A 395 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: A 398 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6400 (tpp-160) REVERT: B 28 GLU cc_start: 0.8132 (tp30) cc_final: 0.7737 (tm-30) REVERT: B 97 ASP cc_start: 0.8357 (m-30) cc_final: 0.7712 (t0) REVERT: B 126 GLU cc_start: 0.7365 (pm20) cc_final: 0.6893 (mm-30) REVERT: B 171 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 233 GLU cc_start: 0.7508 (tt0) cc_final: 0.6955 (mt-10) REVERT: B 398 ARG cc_start: 0.6845 (ttm110) cc_final: 0.5977 (tpp-160) REVERT: C 28 GLU cc_start: 0.8122 (tp30) cc_final: 0.7723 (tm-30) REVERT: C 97 ASP cc_start: 0.8169 (m-30) cc_final: 0.7534 (t0) REVERT: C 126 GLU cc_start: 0.7287 (pm20) cc_final: 0.6841 (mm-30) REVERT: C 189 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8351 (mtpt) REVERT: C 206 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7863 (mttm) REVERT: C 308 LEU cc_start: 0.7812 (mp) cc_final: 0.7531 (tt) REVERT: C 391 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.5048 (tmm) REVERT: D 28 GLU cc_start: 0.7982 (tt0) cc_final: 0.7624 (tm-30) REVERT: D 75 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: D 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7338 (t0) REVERT: D 113 ASP cc_start: 0.8723 (p0) cc_final: 0.8356 (p0) REVERT: D 156 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7623 (mmt) REVERT: D 206 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8012 (mttp) REVERT: D 207 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: D 235 GLN cc_start: 0.8534 (mm110) cc_final: 0.8095 (mt0) REVERT: D 395 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: D 398 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6563 (tpp-160) REVERT: E 28 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7689 (tm-30) REVERT: E 49 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8390 (mtmt) REVERT: E 97 ASP cc_start: 0.8194 (m-30) cc_final: 0.7418 (t0) REVERT: E 126 GLU cc_start: 0.7392 (pm20) cc_final: 0.6896 (mt-10) REVERT: E 179 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (mmt) REVERT: E 233 GLU cc_start: 0.7544 (tt0) cc_final: 0.6957 (mt-10) REVERT: E 236 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7536 (tmm) REVERT: E 395 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: E 398 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6529 (tpp-160) outliers start: 82 outliers final: 43 residues processed: 301 average time/residue: 0.5361 time to fit residues: 176.7695 Evaluate side-chains 301 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 395 PHE Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109790 restraints weight = 17073.525| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.24 r_work: 0.3056 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14495 Z= 0.142 Angle : 0.647 9.473 19715 Z= 0.324 Chirality : 0.044 0.137 2260 Planarity : 0.003 0.038 2430 Dihedral : 4.928 39.958 2192 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.07 % Allowed : 19.08 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.51 (0.19), residues: 1710 helix: -0.59 (0.22), residues: 560 sheet: 0.25 (0.29), residues: 320 loop : -1.81 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.029 0.002 TYR C 238 PHE 0.014 0.001 PHE C 258 TRP 0.009 0.001 TRP D 84 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (14470) covalent geometry : angle 0.64214 / 0.32 (19650) SS BOND : bond 0.00593 / 0.31 ( 10) SS BOND : angle 2.04272 / 1.06 ( 20) hydrogen bonds : bond 0.03415 / 2.28 ( 533) hydrogen bonds : angle 4.14340 / 2.86 ( 1965) link_BETA1-4 : bond 0.00476 / 0.27 ( 10) link_BETA1-4 : angle 1.56216 / 1.03 ( 30) link_NAG-ASN : bond 0.00045 / 0.03 ( 5) link_NAG-ASN : angle 0.64396 / 0.41 ( 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 331 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7602 (tm-30) REVERT: A 36 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8775 (mtpm) REVERT: A 97 ASP cc_start: 0.8058 (m-30) cc_final: 0.7339 (t0) REVERT: A 126 GLU cc_start: 0.7482 (pm20) cc_final: 0.6952 (mt-10) REVERT: A 233 GLU cc_start: 0.7495 (tt0) cc_final: 0.7024 (mt-10) REVERT: A 398 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6302 (tpp-160) REVERT: B 28 GLU cc_start: 0.8112 (tp30) cc_final: 0.7779 (tm-30) REVERT: B 97 ASP cc_start: 0.8366 (m-30) cc_final: 0.7701 (t0) REVERT: B 126 GLU cc_start: 0.7327 (pm20) cc_final: 0.6830 (mm-30) REVERT: B 171 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: B 233 GLU cc_start: 0.7500 (tt0) cc_final: 0.6923 (mt-10) REVERT: B 308 LEU cc_start: 0.7569 (mp) cc_final: 0.7258 (tt) REVERT: B 398 ARG cc_start: 0.6834 (ttm110) cc_final: 0.5920 (tpp-160) REVERT: C 28 GLU cc_start: 0.8111 (tp30) cc_final: 0.7703 (tm-30) REVERT: C 97 ASP cc_start: 0.8159 (m-30) cc_final: 0.7436 (t0) REVERT: C 126 GLU cc_start: 0.7242 (pm20) cc_final: 0.6787 (mm-30) REVERT: C 171 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: C 189 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8316 (mtpt) REVERT: C 206 LYS cc_start: 0.8438 (mtpt) cc_final: 0.7892 (mttm) REVERT: C 225 CYS cc_start: 0.7040 (t) cc_final: 0.6719 (t) REVERT: C 236 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7153 (tmm) REVERT: C 308 LEU cc_start: 0.7757 (mp) cc_final: 0.7513 (tt) REVERT: C 391 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.5019 (tmm) REVERT: D 28 GLU cc_start: 0.7972 (tt0) cc_final: 0.7610 (tm-30) REVERT: D 75 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: D 97 ASP cc_start: 0.8080 (m-30) cc_final: 0.7334 (t0) REVERT: D 113 ASP cc_start: 0.8764 (p0) cc_final: 0.8398 (p0) REVERT: D 126 GLU cc_start: 0.7459 (pm20) cc_final: 0.6861 (mt-10) REVERT: D 156 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7593 (mmt) REVERT: D 207 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: D 233 GLU cc_start: 0.7398 (tt0) cc_final: 0.6954 (mt-10) REVERT: D 235 GLN cc_start: 0.8523 (mm110) cc_final: 0.8098 (mt0) REVERT: D 308 LEU cc_start: 0.7721 (mp) cc_final: 0.7489 (tt) REVERT: D 395 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: D 398 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6507 (tpp-160) REVERT: E 28 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7676 (tm-30) REVERT: E 49 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8411 (mtmt) REVERT: E 97 ASP cc_start: 0.8154 (m-30) cc_final: 0.7473 (t0) REVERT: E 126 GLU cc_start: 0.7420 (pm20) cc_final: 0.6873 (mt-10) REVERT: E 233 GLU cc_start: 0.7526 (tt0) cc_final: 0.6906 (mt-10) REVERT: E 398 ARG cc_start: 0.7174 (ttm110) cc_final: 0.6641 (tpp-160) outliers start: 77 outliers final: 42 residues processed: 288 average time/residue: 0.5393 time to fit residues: 170.5656 Evaluate side-chains 299 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 180 ASN D 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105822 restraints weight = 17155.467| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.20 r_work: 0.3038 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14495 Z= 0.158 Angle : 0.657 9.874 19715 Z= 0.328 Chirality : 0.045 0.144 2260 Planarity : 0.003 0.039 2430 Dihedral : 4.905 45.972 2192 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.00 % Allowed : 19.61 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.36 (0.19), residues: 1710 helix: -0.37 (0.22), residues: 560 sheet: 0.31 (0.29), residues: 320 loop : -1.80 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 229 TYR 0.022 0.002 TYR C 238 PHE 0.014 0.001 PHE C 258 TRP 0.009 0.001 TRP B 84 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (14470) covalent geometry : angle 0.65153 / 0.33 (19650) SS BOND : bond 0.00507 / 0.28 ( 10) SS BOND : angle 2.10417 / 1.09 ( 20) hydrogen bonds : bond 0.03452 / 2.31 ( 533) hydrogen bonds : angle 4.13057 / 2.85 ( 1965) link_BETA1-4 : bond 0.00479 / 0.28 ( 10) link_BETA1-4 : angle 1.48831 / 0.97 ( 30) link_NAG-ASN : bond 0.00055 / 0.03 ( 5) link_NAG-ASN : angle 0.64027 / 0.41 ( 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 315 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 239 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7658 (tm-30) REVERT: A 36 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8768 (mtpm) REVERT: A 97 ASP cc_start: 0.8049 (m-30) cc_final: 0.7351 (t0) REVERT: A 126 GLU cc_start: 0.7539 (pm20) cc_final: 0.7000 (mt-10) REVERT: A 233 GLU cc_start: 0.7497 (tt0) cc_final: 0.7033 (mt-10) REVERT: A 395 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: A 398 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6353 (tpp-160) REVERT: B 28 GLU cc_start: 0.8095 (tp30) cc_final: 0.7804 (tm-30) REVERT: B 97 ASP cc_start: 0.8372 (m-30) cc_final: 0.7708 (t0) REVERT: B 126 GLU cc_start: 0.7347 (pm20) cc_final: 0.6863 (mm-30) REVERT: B 171 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 207 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8325 (tp30) REVERT: B 233 GLU cc_start: 0.7537 (tt0) cc_final: 0.6948 (mt-10) REVERT: B 308 LEU cc_start: 0.7555 (mp) cc_final: 0.7257 (tt) REVERT: B 398 ARG cc_start: 0.6845 (ttm110) cc_final: 0.5903 (tpp-160) REVERT: C 28 GLU cc_start: 0.8085 (tp30) cc_final: 0.7679 (tm-30) REVERT: C 97 ASP cc_start: 0.8178 (m-30) cc_final: 0.7489 (t0) REVERT: C 156 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8251 (mmt) REVERT: C 189 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8475 (mtpt) REVERT: C 206 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7859 (mttm) REVERT: C 236 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7200 (tmm) REVERT: C 308 LEU cc_start: 0.7768 (mp) cc_final: 0.7531 (tt) REVERT: C 391 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.5028 (tmm) REVERT: D 28 GLU cc_start: 0.7992 (tt0) cc_final: 0.7647 (tm-30) REVERT: D 75 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7650 (ttm-80) REVERT: D 97 ASP cc_start: 0.8092 (m-30) cc_final: 0.7345 (t0) REVERT: D 113 ASP cc_start: 0.8816 (p0) cc_final: 0.8458 (p0) REVERT: D 126 GLU cc_start: 0.7473 (pm20) cc_final: 0.6895 (mt-10) REVERT: D 156 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7654 (mmt) REVERT: D 207 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: D 233 GLU cc_start: 0.7560 (tt0) cc_final: 0.7009 (mt-10) REVERT: D 235 GLN cc_start: 0.8482 (mm110) cc_final: 0.8030 (mt0) REVERT: D 395 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: D 398 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6532 (tpp-160) REVERT: E 28 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7693 (tm-30) REVERT: E 49 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8440 (mtmt) REVERT: E 97 ASP cc_start: 0.8093 (m-30) cc_final: 0.7472 (t0) REVERT: E 126 GLU cc_start: 0.7417 (pm20) cc_final: 0.6893 (mt-10) REVERT: E 233 GLU cc_start: 0.7559 (tt0) cc_final: 0.6939 (mt-10) REVERT: E 308 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7404 (tt) REVERT: E 395 PHE cc_start: 0.5922 (m-80) cc_final: 0.5720 (m-10) REVERT: E 398 ARG cc_start: 0.7450 (ttm110) cc_final: 0.6800 (tpp-160) outliers start: 76 outliers final: 47 residues processed: 279 average time/residue: 0.5211 time to fit residues: 160.1910 Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 157 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 119 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN D 82 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109166 restraints weight = 16968.526| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.16 r_work: 0.3090 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14495 Z= 0.114 Angle : 0.633 11.378 19715 Z= 0.313 Chirality : 0.044 0.156 2260 Planarity : 0.003 0.037 2430 Dihedral : 4.682 45.501 2192 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.68 % Allowed : 20.79 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.20 (0.19), residues: 1710 helix: -0.06 (0.22), residues: 570 sheet: 0.39 (0.29), residues: 320 loop : -1.85 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.029 0.001 TYR D 238 PHE 0.013 0.001 PHE C 258 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14470) covalent geometry : angle 0.62891 / 0.31 (19650) SS BOND : bond 0.00412 / 0.22 ( 10) SS BOND : angle 1.81443 / 0.93 ( 20) hydrogen bonds : bond 0.03206 / 2.16 ( 533) hydrogen bonds : angle 3.95301 / 2.73 ( 1965) link_BETA1-4 : bond 0.00479 / 0.27 ( 10) link_BETA1-4 : angle 1.40753 / 0.89 ( 30) link_NAG-ASN : bond 0.00184 / 0.11 ( 5) link_NAG-ASN : angle 0.57619 / 0.35 ( 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 309 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7703 (tm-30) REVERT: A 36 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8765 (mtpm) REVERT: A 58 ASN cc_start: 0.8074 (p0) cc_final: 0.7846 (p0) REVERT: A 97 ASP cc_start: 0.8044 (m-30) cc_final: 0.7363 (t0) REVERT: A 126 GLU cc_start: 0.7517 (pm20) cc_final: 0.6975 (mt-10) REVERT: A 308 LEU cc_start: 0.7519 (mp) cc_final: 0.7306 (tt) REVERT: A 391 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.4164 (tmt) REVERT: A 398 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6279 (tpp-160) REVERT: B 28 GLU cc_start: 0.8073 (tp30) cc_final: 0.7760 (tm-30) REVERT: B 97 ASP cc_start: 0.8320 (m-30) cc_final: 0.7693 (t0) REVERT: B 308 LEU cc_start: 0.7572 (mp) cc_final: 0.7348 (tt) REVERT: B 398 ARG cc_start: 0.6782 (ttm110) cc_final: 0.5834 (tpp-160) REVERT: C 28 GLU cc_start: 0.8054 (tp30) cc_final: 0.7669 (tm-30) REVERT: C 97 ASP cc_start: 0.8130 (m-30) cc_final: 0.7501 (t0) REVERT: C 189 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8463 (mtpt) REVERT: C 206 LYS cc_start: 0.8437 (mtpt) cc_final: 0.7892 (mttm) REVERT: C 225 CYS cc_start: 0.7255 (t) cc_final: 0.7001 (t) REVERT: C 391 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.5014 (tmm) REVERT: D 28 GLU cc_start: 0.8009 (tt0) cc_final: 0.7695 (tm-30) REVERT: D 75 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7595 (ttm-80) REVERT: D 97 ASP cc_start: 0.8035 (m-30) cc_final: 0.7337 (t0) REVERT: D 113 ASP cc_start: 0.8803 (p0) cc_final: 0.8448 (p0) REVERT: D 156 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7503 (mmt) REVERT: D 207 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: D 235 GLN cc_start: 0.8520 (mm110) cc_final: 0.8058 (mt0) REVERT: D 395 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: D 398 ARG cc_start: 0.7212 (ttm110) cc_final: 0.6471 (tpp-160) REVERT: E 28 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7681 (tm-30) REVERT: E 49 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8449 (mtmt) REVERT: E 97 ASP cc_start: 0.8071 (m-30) cc_final: 0.7482 (t0) REVERT: E 163 MET cc_start: 0.8378 (mtm) cc_final: 0.7944 (mpp) REVERT: E 171 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: E 398 ARG cc_start: 0.7417 (ttm110) cc_final: 0.6768 (tpp-160) outliers start: 56 outliers final: 39 residues processed: 281 average time/residue: 0.5240 time to fit residues: 162.0852 Evaluate side-chains 286 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 131 ASN D 62 ASN D 131 ASN D 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108223 restraints weight = 17060.622| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.20 r_work: 0.3076 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14495 Z= 0.132 Angle : 0.659 11.941 19715 Z= 0.326 Chirality : 0.044 0.151 2260 Planarity : 0.003 0.037 2430 Dihedral : 4.660 45.456 2192 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.55 % Allowed : 21.64 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.11 (0.19), residues: 1710 helix: 0.05 (0.23), residues: 570 sheet: 0.46 (0.30), residues: 320 loop : -1.84 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 229 TYR 0.019 0.001 TYR C 238 PHE 0.014 0.001 PHE C 258 TRP 0.009 0.001 TRP D 84 HIS 0.001 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14470) covalent geometry : angle 0.65513 / 0.32 (19650) SS BOND : bond 0.00461 / 0.25 ( 10) SS BOND : angle 1.89023 / 0.98 ( 20) hydrogen bonds : bond 0.03253 / 2.19 ( 533) hydrogen bonds : angle 3.94798 / 2.73 ( 1965) link_BETA1-4 : bond 0.00488 / 0.28 ( 10) link_BETA1-4 : angle 1.39181 / 0.89 ( 30) link_NAG-ASN : bond 0.00082 / 0.05 ( 5) link_NAG-ASN : angle 0.55517 / 0.36 ( 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 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7664 (tm-30) REVERT: A 36 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8785 (mtpp) REVERT: A 58 ASN cc_start: 0.8109 (p0) cc_final: 0.7888 (p0) REVERT: A 97 ASP cc_start: 0.8045 (m-30) cc_final: 0.7330 (t0) REVERT: A 308 LEU cc_start: 0.7499 (mp) cc_final: 0.7285 (tt) REVERT: A 398 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6209 (tpp-160) REVERT: B 28 GLU cc_start: 0.8057 (tp30) cc_final: 0.7740 (tm-30) REVERT: B 97 ASP cc_start: 0.8310 (m-30) cc_final: 0.7675 (t0) REVERT: B 233 GLU cc_start: 0.7634 (tt0) cc_final: 0.7044 (mt-10) REVERT: B 308 LEU cc_start: 0.7572 (mp) cc_final: 0.7348 (tt) REVERT: B 398 ARG cc_start: 0.6766 (ttm110) cc_final: 0.5795 (tpp-160) REVERT: C 28 GLU cc_start: 0.7994 (tp30) cc_final: 0.7582 (tm-30) REVERT: C 97 ASP cc_start: 0.8105 (m-30) cc_final: 0.7499 (t0) REVERT: C 189 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: C 206 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7859 (mttm) REVERT: C 225 CYS cc_start: 0.7254 (t) cc_final: 0.7009 (t) REVERT: C 391 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4918 (tmm) REVERT: D 28 GLU cc_start: 0.8000 (tt0) cc_final: 0.7677 (tm-30) REVERT: D 75 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7567 (ttm-80) REVERT: D 97 ASP cc_start: 0.7968 (m-30) cc_final: 0.7280 (t0) REVERT: D 113 ASP cc_start: 0.8810 (p0) cc_final: 0.8447 (p0) REVERT: D 126 GLU cc_start: 0.7463 (pm20) cc_final: 0.6880 (mt-10) REVERT: D 156 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7461 (mmt) REVERT: D 207 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8081 (tm-30) REVERT: D 233 GLU cc_start: 0.7515 (tt0) cc_final: 0.6964 (mt-10) REVERT: D 235 GLN cc_start: 0.8461 (mm110) cc_final: 0.7991 (mt0) REVERT: D 395 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: D 398 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6468 (tpp-160) REVERT: E 28 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7698 (tm-30) REVERT: E 49 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8454 (mtmt) REVERT: E 97 ASP cc_start: 0.8054 (m-30) cc_final: 0.7475 (t0) REVERT: E 126 GLU cc_start: 0.7436 (pm20) cc_final: 0.6921 (mm-30) REVERT: E 163 MET cc_start: 0.8397 (mtm) cc_final: 0.7967 (mpp) REVERT: E 171 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: E 398 ARG cc_start: 0.7371 (ttm110) cc_final: 0.6836 (tpp-160) outliers start: 54 outliers final: 41 residues processed: 271 average time/residue: 0.5292 time to fit residues: 157.9906 Evaluate side-chains 285 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN D 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108139 restraints weight = 17055.218| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.20 r_work: 0.3080 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14495 Z= 0.133 Angle : 0.670 11.312 19715 Z= 0.332 Chirality : 0.044 0.163 2260 Planarity : 0.003 0.036 2430 Dihedral : 4.657 44.664 2192 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.16 % Allowed : 21.97 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.05 (0.20), residues: 1710 helix: 0.12 (0.23), residues: 580 sheet: 0.44 (0.29), residues: 320 loop : -1.82 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 229 TYR 0.033 0.001 TYR D 238 PHE 0.014 0.001 PHE C 258 TRP 0.009 0.001 TRP A 84 HIS 0.002 0.000 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (14470) covalent geometry : angle 0.66617 / 0.33 (19650) SS BOND : bond 0.00442 / 0.24 ( 10) SS BOND : angle 1.89221 / 0.98 ( 20) hydrogen bonds : bond 0.03224 / 2.18 ( 533) hydrogen bonds : angle 3.94746 / 2.74 ( 1965) link_BETA1-4 : bond 0.00482 / 0.27 ( 10) link_BETA1-4 : angle 1.36620 / 0.87 ( 30) link_NAG-ASN : bond 0.00104 / 0.06 ( 5) link_NAG-ASN : angle 0.52773 / 0.33 ( 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 275 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7668 (tm-30) REVERT: A 36 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8786 (mtpp) REVERT: A 58 ASN cc_start: 0.8126 (p0) cc_final: 0.7885 (p0) REVERT: A 97 ASP cc_start: 0.8036 (m-30) cc_final: 0.7327 (t0) REVERT: A 398 ARG cc_start: 0.7038 (ttm110) cc_final: 0.6259 (tpp-160) REVERT: B 28 GLU cc_start: 0.8069 (tp30) cc_final: 0.7739 (tm-30) REVERT: B 97 ASP cc_start: 0.8306 (m-30) cc_final: 0.7674 (t0) REVERT: B 308 LEU cc_start: 0.7570 (mp) cc_final: 0.7363 (tt) REVERT: B 398 ARG cc_start: 0.6760 (ttm110) cc_final: 0.5788 (tpp-160) REVERT: C 28 GLU cc_start: 0.7977 (tp30) cc_final: 0.7557 (tm-30) REVERT: C 97 ASP cc_start: 0.8098 (m-30) cc_final: 0.7498 (t0) REVERT: C 189 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (mtpt) REVERT: C 206 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7853 (mttm) REVERT: C 225 CYS cc_start: 0.7240 (t) cc_final: 0.7004 (t) REVERT: C 391 MET cc_start: 0.5198 (OUTLIER) cc_final: 0.4915 (tmm) REVERT: D 28 GLU cc_start: 0.8000 (tt0) cc_final: 0.7676 (tm-30) REVERT: D 75 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7551 (ttm-80) REVERT: D 97 ASP cc_start: 0.7948 (m-30) cc_final: 0.7273 (t0) REVERT: D 113 ASP cc_start: 0.8811 (p0) cc_final: 0.8451 (p0) REVERT: D 126 GLU cc_start: 0.7450 (pm20) cc_final: 0.6889 (mt-10) REVERT: D 156 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7469 (mmt) REVERT: D 207 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8059 (tm-30) REVERT: D 233 GLU cc_start: 0.7512 (tt0) cc_final: 0.6930 (mt-10) REVERT: D 395 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: D 398 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6457 (tpp-160) REVERT: E 28 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7622 (tm-30) REVERT: E 49 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8410 (mtmm) REVERT: E 97 ASP cc_start: 0.8042 (m-30) cc_final: 0.7461 (t0) REVERT: E 171 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: E 398 ARG cc_start: 0.7323 (ttm110) cc_final: 0.6772 (tpp-160) outliers start: 48 outliers final: 38 residues processed: 253 average time/residue: 0.5366 time to fit residues: 149.5614 Evaluate side-chains 269 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108639 restraints weight = 17002.415| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.21 r_work: 0.3086 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14495 Z= 0.127 Angle : 0.662 11.164 19715 Z= 0.327 Chirality : 0.044 0.156 2260 Planarity : 0.003 0.036 2430 Dihedral : 4.578 44.617 2190 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.09 % Allowed : 22.17 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.20), residues: 1710 helix: 0.20 (0.23), residues: 580 sheet: 0.46 (0.29), residues: 320 loop : -1.80 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 229 TYR 0.018 0.001 TYR C 238 PHE 0.013 0.001 PHE C 258 TRP 0.009 0.001 TRP D 84 HIS 0.001 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14470) covalent geometry : angle 0.65838 / 0.33 (19650) SS BOND : bond 0.00430 / 0.23 ( 10) SS BOND : angle 1.85204 / 0.96 ( 20) hydrogen bonds : bond 0.03173 / 2.15 ( 533) hydrogen bonds : angle 3.91880 / 2.71 ( 1965) link_BETA1-4 : bond 0.00481 / 0.28 ( 10) link_BETA1-4 : angle 1.35225 / 0.85 ( 30) link_NAG-ASN : bond 0.00105 / 0.06 ( 5) link_NAG-ASN : angle 0.50235 / 0.31 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.70 seconds wall clock time: 78 minutes 3.60 seconds (4683.60 seconds total)