Starting phenix.real_space_refine on Sat Sep 12 06:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm2_20384/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_2026/6pm2_20384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm2_20384/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: 2.65, per 1000 atoms: 0.19 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 620.7 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: 0.34 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: 2.06 Time building geometry restraints manager: 1.44 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 - 14.69: 8066 14.69 - 29.39: 377 29.39 - 44.08: 72 44.08 - 58.78: 5 58.78 - 73.47: 5 Dihedral angle restraints: 8525 sinusoidal: 3410 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 8522 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.740 Find NCS groups from input model: 0.130 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 9.076 73.474 5175 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 : 0.528 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: 0.5160 time to fit residues: 259.5213 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 : 0.466 ------------------------------------------------------------------------------- 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... 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 = 0.3783 r_free = 0.3783 target = 0.146917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112797 restraints weight = 17520.491| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.09 r_work: 0.3188 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2562 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 : 0.702 7.442 19715 Z= 0.365 Chirality : 0.046 0.146 2260 Planarity : 0.005 0.043 2430 Dihedral : 5.524 24.924 1889 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.47 % Allowed : 13.03 % Favored : 82.50 % 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: -3.58 (0.16), residues: 1710 helix: -2.87 (0.16), residues: 575 sheet: -1.12 (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 C 229 TYR 0.026 0.002 TYR D 238 PHE 0.016 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 0.00394 / 0.17 (14470) covalent geometry : angle 0.69831 / 0.36 (19650) SS BOND : bond 0.00524 / 0.29 ( 10) SS BOND : angle 1.61887 / 0.95 ( 20) hydrogen bonds : bond 0.05112 / 3.40 ( 533) hydrogen bonds : angle 5.43994 / 3.73 ( 1965) link_BETA1-4 : bond 0.00512 / 0.30 ( 10) link_BETA1-4 : angle 1.46312 / 0.88 ( 30) link_NAG-ASN : bond 0.00268 / 0.15 ( 5) link_NAG-ASN : angle 0.47706 / 0.31 ( 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 355 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 287 time to evaluate : 0.479 Fit side-chains REVERT: A 71 THR cc_start: 0.9261 (p) cc_final: 0.8892 (p) REVERT: A 72 MET cc_start: 0.9110 (mtt) cc_final: 0.8748 (mtt) REVERT: A 126 GLU cc_start: 0.7542 (pm20) cc_final: 0.7201 (mt-10) REVERT: A 207 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8149 (pt0) REVERT: A 227 GLU cc_start: 0.8774 (pt0) cc_final: 0.8505 (pt0) REVERT: A 233 GLU cc_start: 0.7565 (tt0) cc_final: 0.7065 (mt-10) REVERT: A 391 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.3642 (tmm) REVERT: A 398 ARG cc_start: 0.7158 (ttm110) cc_final: 0.6478 (tpp-160) REVERT: B 28 GLU cc_start: 0.8177 (tp30) cc_final: 0.7677 (tm-30) REVERT: B 126 GLU cc_start: 0.7644 (pm20) cc_final: 0.7279 (mt-10) REVERT: B 398 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6303 (tpp-160) REVERT: C 28 GLU cc_start: 0.8194 (tp30) cc_final: 0.7779 (tm-30) REVERT: C 227 GLU cc_start: 0.8728 (pt0) cc_final: 0.8283 (pt0) REVERT: D 28 GLU cc_start: 0.8157 (tt0) cc_final: 0.7699 (tm-30) REVERT: D 75 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: D 113 ASP cc_start: 0.8659 (p0) cc_final: 0.8418 (p0) REVERT: D 126 GLU cc_start: 0.7661 (pm20) cc_final: 0.7296 (mt-10) REVERT: D 206 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8177 (mttp) REVERT: D 235 GLN cc_start: 0.8579 (mm110) cc_final: 0.8170 (mt0) REVERT: D 398 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6529 (tpp-160) REVERT: D 400 LYS cc_start: 0.6624 (tmtp) cc_final: 0.6304 (tmmt) REVERT: E 49 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: E 126 GLU cc_start: 0.7543 (pm20) cc_final: 0.7204 (mt-10) REVERT: E 210 ASP cc_start: 0.8195 (m-30) cc_final: 0.7730 (m-30) REVERT: E 398 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6494 (tpp-160) outliers start: 68 outliers final: 26 residues processed: 328 average time/residue: 0.5616 time to fit residues: 202.4718 Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 56 THR 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: 0.0040 chunk 102 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 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: 4.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 E 85 ASN E 141 ASN E 261 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105246 restraints weight = 17793.493| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.05 r_work: 0.3035 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14495 Z= 0.255 Angle : 0.753 10.690 19715 Z= 0.379 Chirality : 0.048 0.155 2260 Planarity : 0.005 0.040 2430 Dihedral : 5.589 26.258 1887 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.79 % Allowed : 14.01 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.18), residues: 1710 helix: -1.72 (0.21), residues: 540 sheet: -0.61 (0.27), residues: 345 loop : -2.24 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 229 TYR 0.023 0.002 TYR C 238 PHE 0.016 0.002 PHE D 124 TRP 0.014 0.002 TRP D 422 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (14470) covalent geometry : angle 0.74902 / 0.38 (19650) SS BOND : bond 0.00688 / 0.39 ( 10) SS BOND : angle 1.95916 / 1.17 ( 20) hydrogen bonds : bond 0.04532 / 3.01 ( 533) hydrogen bonds : angle 4.94184 / 3.40 ( 1965) link_BETA1-4 : bond 0.00813 / 0.46 ( 10) link_BETA1-4 : angle 1.52378 / 0.95 ( 30) link_NAG-ASN : bond 0.00136 / 0.08 ( 5) link_NAG-ASN : angle 0.74404 / 0.49 ( 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 361 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 0.537 Fit side-chains REVERT: A 28 GLU cc_start: 0.8032 (tt0) cc_final: 0.7426 (tm-30) REVERT: A 71 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8866 (p) REVERT: A 72 MET cc_start: 0.9145 (mtt) cc_final: 0.8808 (mtt) REVERT: A 126 GLU cc_start: 0.7591 (pm20) cc_final: 0.7217 (mt-10) REVERT: A 233 GLU cc_start: 0.7712 (tt0) cc_final: 0.7228 (mt-10) REVERT: A 236 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7666 (tmm) REVERT: A 391 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.4338 (tmt) REVERT: A 398 ARG cc_start: 0.7383 (ttm110) cc_final: 0.6581 (tpp-160) REVERT: A 401 ARG cc_start: 0.5259 (OUTLIER) cc_final: 0.5057 (tpt-90) REVERT: B 28 GLU cc_start: 0.8173 (tp30) cc_final: 0.7770 (tm-30) REVERT: B 97 ASP cc_start: 0.8321 (m-30) cc_final: 0.7673 (t0) REVERT: B 126 GLU cc_start: 0.7625 (pm20) cc_final: 0.7296 (mt-10) REVERT: B 233 GLU cc_start: 0.7741 (tt0) cc_final: 0.7197 (mt-10) REVERT: B 398 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6253 (tpp-160) REVERT: C 28 GLU cc_start: 0.8255 (tp30) cc_final: 0.7808 (tm-30) REVERT: C 49 LYS cc_start: 0.8744 (mmpt) cc_final: 0.8468 (mtmt) REVERT: C 126 GLU cc_start: 0.7500 (pm20) cc_final: 0.7279 (mm-30) REVERT: C 189 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8566 (mtpt) REVERT: C 206 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8137 (mttm) REVERT: C 210 ASP cc_start: 0.8141 (m-30) cc_final: 0.7936 (m-30) REVERT: C 227 GLU cc_start: 0.8811 (pt0) cc_final: 0.8542 (pt0) REVERT: C 229 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (mmm-85) REVERT: C 391 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5165 (tmm) REVERT: D 28 GLU cc_start: 0.8135 (tt0) cc_final: 0.7688 (tm-30) REVERT: D 75 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7668 (ttm-80) REVERT: D 113 ASP cc_start: 0.8785 (p0) cc_final: 0.8399 (p0) REVERT: D 126 GLU cc_start: 0.7662 (pm20) cc_final: 0.7285 (mt-10) REVERT: D 206 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8195 (mttp) REVERT: D 227 GLU cc_start: 0.8807 (pt0) cc_final: 0.8510 (pt0) REVERT: D 235 GLN cc_start: 0.8530 (mm110) cc_final: 0.8091 (mt0) REVERT: D 236 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: D 395 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: D 398 ARG cc_start: 0.7352 (ttm110) cc_final: 0.6618 (tpp-160) REVERT: D 400 LYS cc_start: 0.6633 (tmtp) cc_final: 0.6211 (tmmt) REVERT: E 24 MET cc_start: 0.8343 (tpt) cc_final: 0.8059 (tpt) REVERT: E 49 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8453 (mtmt) REVERT: E 126 GLU cc_start: 0.7522 (pm20) cc_final: 0.7197 (mt-10) REVERT: E 233 GLU cc_start: 0.7716 (tt0) cc_final: 0.7168 (mt-10) REVERT: E 391 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.4403 (tmm) REVERT: E 398 ARG cc_start: 0.7423 (ttm110) cc_final: 0.6593 (tpp-160) REVERT: E 418 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8286 (m110) outliers start: 88 outliers final: 40 residues processed: 320 average time/residue: 0.5695 time to fit residues: 200.4287 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 GLN 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 301 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 401 ARG 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 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 229 ARG Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 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 34 MET Chi-restraints excluded: chain D residue 37 VAL 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 283 SER 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 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 301 ILE Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 261 ASN B 131 ASN B 261 ASN C 82 GLN C 261 ASN D 62 ASN D 180 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108551 restraints weight = 17715.412| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.04 r_work: 0.3079 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14495 Z= 0.144 Angle : 0.649 7.550 19715 Z= 0.330 Chirality : 0.045 0.149 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.243 22.535 1887 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.21 % Allowed : 17.50 % Favored : 78.29 % 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: -2.16 (0.19), residues: 1710 helix: -1.22 (0.22), residues: 560 sheet: -0.30 (0.28), residues: 345 loop : -2.08 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 229 TYR 0.025 0.002 TYR D 238 PHE 0.011 0.001 PHE D 115 TRP 0.009 0.001 TRP C 422 HIS 0.001 0.000 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14470) covalent geometry : angle 0.64517 / 0.33 (19650) SS BOND : bond 0.00523 / 0.29 ( 10) SS BOND : angle 1.56072 / 0.92 ( 20) hydrogen bonds : bond 0.03810 / 2.54 ( 533) hydrogen bonds : angle 4.46056 / 3.06 ( 1965) link_BETA1-4 : bond 0.00573 / 0.32 ( 10) link_BETA1-4 : angle 1.45704 / 0.90 ( 30) link_NAG-ASN : bond 0.00193 / 0.11 ( 5) link_NAG-ASN : angle 0.57589 / 0.37 ( 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 337 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8005 (tt0) cc_final: 0.7447 (tm-30) REVERT: A 97 ASP cc_start: 0.8095 (m-30) cc_final: 0.7321 (t0) REVERT: A 126 GLU cc_start: 0.7532 (pm20) cc_final: 0.7162 (mt-10) REVERT: A 233 GLU cc_start: 0.7617 (tt0) cc_final: 0.7201 (mt-10) REVERT: A 398 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6546 (tpp-160) REVERT: A 401 ARG cc_start: 0.5187 (OUTLIER) cc_final: 0.4986 (tpt-90) REVERT: B 28 GLU cc_start: 0.8188 (tp30) cc_final: 0.7783 (tm-30) REVERT: B 97 ASP cc_start: 0.8323 (m-30) cc_final: 0.7706 (t0) REVERT: B 126 GLU cc_start: 0.7639 (pm20) cc_final: 0.7277 (mt-10) REVERT: B 398 ARG cc_start: 0.7068 (ttm110) cc_final: 0.6164 (tpp-160) REVERT: C 28 GLU cc_start: 0.8188 (tp30) cc_final: 0.7749 (tm-30) REVERT: C 49 LYS cc_start: 0.8747 (mmpt) cc_final: 0.8468 (mtmt) REVERT: C 97 ASP cc_start: 0.8172 (m-30) cc_final: 0.7560 (t0) REVERT: C 189 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8490 (mtpt) REVERT: C 206 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8143 (mttm) REVERT: C 227 GLU cc_start: 0.8758 (pt0) cc_final: 0.8439 (pt0) REVERT: C 391 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.5039 (tmm) REVERT: D 28 GLU cc_start: 0.8111 (tt0) cc_final: 0.7667 (tm-30) REVERT: D 75 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7658 (ttm-80) REVERT: D 97 ASP cc_start: 0.8125 (m-30) cc_final: 0.7396 (t0) REVERT: D 113 ASP cc_start: 0.8748 (p0) cc_final: 0.8378 (p0) REVERT: D 126 GLU cc_start: 0.7613 (pm20) cc_final: 0.7194 (mt-10) REVERT: D 233 GLU cc_start: 0.7498 (tt0) cc_final: 0.7045 (mt-10) REVERT: D 235 GLN cc_start: 0.8599 (mm110) cc_final: 0.8156 (mt0) REVERT: D 398 ARG cc_start: 0.7362 (ttm110) cc_final: 0.6645 (tpp-160) REVERT: E 28 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7777 (tm-30) REVERT: E 49 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8444 (mtmm) REVERT: E 126 GLU cc_start: 0.7509 (pm20) cc_final: 0.7183 (mt-10) REVERT: E 233 GLU cc_start: 0.7630 (tt0) cc_final: 0.7170 (mt-10) REVERT: E 391 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.4520 (tmm) REVERT: E 398 ARG cc_start: 0.7425 (ttm110) cc_final: 0.6597 (tpp-160) outliers start: 64 outliers final: 30 residues processed: 299 average time/residue: 0.5536 time to fit residues: 182.3249 Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 401 ARG 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 B residue 404 THR 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 129 THR Chi-restraints excluded: chain C residue 189 LYS 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 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 391 MET 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 214 CYS Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 391 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 62 ASN A 82 GLN A 180 ASN B 58 ASN B 82 GLN C 58 ASN C 62 ASN D 62 ASN D 82 GLN E 58 ASN E 418 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110063 restraints weight = 17557.303| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.04 r_work: 0.3104 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3607 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= 0.124 Angle : 0.625 9.486 19715 Z= 0.317 Chirality : 0.044 0.151 2260 Planarity : 0.003 0.037 2430 Dihedral : 4.961 21.475 1887 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.47 % Allowed : 18.16 % Favored : 77.37 % 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: -1.87 (0.19), residues: 1710 helix: -0.88 (0.22), residues: 555 sheet: -0.22 (0.28), residues: 345 loop : -1.95 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 229 TYR 0.029 0.001 TYR C 238 PHE 0.012 0.001 PHE D 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 0.00287 / 0.12 (14470) covalent geometry : angle 0.62220 / 0.32 (19650) SS BOND : bond 0.00460 / 0.25 ( 10) SS BOND : angle 1.41567 / 0.84 ( 20) hydrogen bonds : bond 0.03516 / 2.35 ( 533) hydrogen bonds : angle 4.19130 / 2.88 ( 1965) link_BETA1-4 : bond 0.00554 / 0.31 ( 10) link_BETA1-4 : angle 1.42593 / 0.88 ( 30) link_NAG-ASN : bond 0.00169 / 0.10 ( 5) link_NAG-ASN : angle 0.54766 / 0.35 ( 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 331 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7927 (tt0) cc_final: 0.7412 (tm-30) REVERT: A 97 ASP cc_start: 0.8074 (m-30) cc_final: 0.7383 (t0) REVERT: A 126 GLU cc_start: 0.7533 (pm20) cc_final: 0.7149 (mt-10) REVERT: A 233 GLU cc_start: 0.7646 (tt0) cc_final: 0.7180 (mt-10) REVERT: A 398 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6450 (tpp-160) REVERT: B 28 GLU cc_start: 0.8168 (tp30) cc_final: 0.7796 (tm-30) REVERT: B 97 ASP cc_start: 0.8306 (m-30) cc_final: 0.7753 (t0) REVERT: B 126 GLU cc_start: 0.7567 (pm20) cc_final: 0.7220 (mm-30) REVERT: B 170 MET cc_start: 0.8931 (ptp) cc_final: 0.8699 (ptp) REVERT: B 171 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: B 398 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6134 (tpp-160) REVERT: C 28 GLU cc_start: 0.8135 (tp30) cc_final: 0.7750 (tm-30) REVERT: C 49 LYS cc_start: 0.8761 (mmpt) cc_final: 0.8487 (mtmt) REVERT: C 97 ASP cc_start: 0.8187 (m-30) cc_final: 0.7633 (t0) REVERT: C 126 GLU cc_start: 0.7386 (pm20) cc_final: 0.7048 (mm-30) REVERT: C 189 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: C 206 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8119 (mttm) REVERT: C 308 LEU cc_start: 0.7961 (mp) cc_final: 0.7667 (tt) REVERT: C 391 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.5046 (tmm) REVERT: D 28 GLU cc_start: 0.8094 (tt0) cc_final: 0.7743 (tm-30) REVERT: D 75 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: D 97 ASP cc_start: 0.8110 (m-30) cc_final: 0.7412 (t0) REVERT: D 113 ASP cc_start: 0.8709 (p0) cc_final: 0.8323 (p0) REVERT: D 156 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.7720 (mmt) REVERT: D 233 GLU cc_start: 0.7506 (tt0) cc_final: 0.7133 (mt-10) REVERT: D 235 GLN cc_start: 0.8630 (mm110) cc_final: 0.8206 (mt0) REVERT: D 398 ARG cc_start: 0.7404 (ttm110) cc_final: 0.6703 (tpp-160) REVERT: E 28 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7758 (tm-30) REVERT: E 49 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8455 (mtmm) REVERT: E 97 ASP cc_start: 0.8175 (m-30) cc_final: 0.7497 (t0) REVERT: E 126 GLU cc_start: 0.7448 (pm20) cc_final: 0.7077 (mt-10) REVERT: E 398 ARG cc_start: 0.7384 (ttm110) cc_final: 0.6603 (tpp-160) outliers start: 68 outliers final: 45 residues processed: 297 average time/residue: 0.5748 time to fit residues: 187.9174 Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 214 CYS 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 395 PHE Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 408 VAL 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 219 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER 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: 0.8980 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN B 62 ASN C 131 ASN D 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109139 restraints weight = 17479.803| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.05 r_work: 0.3091 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14495 Z= 0.139 Angle : 0.636 9.548 19715 Z= 0.320 Chirality : 0.044 0.150 2260 Planarity : 0.003 0.040 2430 Dihedral : 4.871 20.802 1887 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.20 % Allowed : 18.75 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.19), residues: 1710 helix: -0.67 (0.22), residues: 565 sheet: -0.13 (0.28), residues: 345 loop : -1.92 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 229 TYR 0.029 0.001 TYR D 238 PHE 0.013 0.001 PHE C 258 TRP 0.010 0.001 TRP C 422 HIS 0.002 0.000 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (14470) covalent geometry : angle 0.63282 / 0.32 (19650) SS BOND : bond 0.00513 / 0.28 ( 10) SS BOND : angle 1.53022 / 0.89 ( 20) hydrogen bonds : bond 0.03399 / 2.28 ( 533) hydrogen bonds : angle 4.10618 / 2.82 ( 1965) link_BETA1-4 : bond 0.00583 / 0.33 ( 10) link_BETA1-4 : angle 1.42478 / 0.87 ( 30) link_NAG-ASN : bond 0.00138 / 0.08 ( 5) link_NAG-ASN : angle 0.54309 / 0.35 ( 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 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7878 (tt0) cc_final: 0.7467 (tm-30) REVERT: A 36 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8724 (mtpm) REVERT: A 97 ASP cc_start: 0.8078 (m-30) cc_final: 0.7441 (t0) REVERT: A 126 GLU cc_start: 0.7568 (pm20) cc_final: 0.7147 (mt-10) REVERT: A 233 GLU cc_start: 0.7621 (tt0) cc_final: 0.7186 (mt-10) REVERT: A 395 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 398 ARG cc_start: 0.7258 (ttm110) cc_final: 0.6456 (tpp-160) REVERT: B 28 GLU cc_start: 0.8151 (tp30) cc_final: 0.7775 (tm-30) REVERT: B 97 ASP cc_start: 0.8330 (m-30) cc_final: 0.7764 (t0) REVERT: B 126 GLU cc_start: 0.7452 (pm20) cc_final: 0.7049 (mm-30) REVERT: B 171 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8395 (mt0) REVERT: B 233 GLU cc_start: 0.7677 (tt0) cc_final: 0.7138 (mt-10) REVERT: B 398 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6009 (tpp-160) REVERT: C 28 GLU cc_start: 0.8124 (tp30) cc_final: 0.7732 (tm-30) REVERT: C 97 ASP cc_start: 0.8174 (m-30) cc_final: 0.7630 (t0) REVERT: C 126 GLU cc_start: 0.7345 (pm20) cc_final: 0.7002 (mm-30) REVERT: C 189 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8377 (mtpt) REVERT: C 206 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8091 (mttm) REVERT: C 308 LEU cc_start: 0.7877 (mp) cc_final: 0.7601 (tt) REVERT: C 391 MET cc_start: 0.5282 (OUTLIER) cc_final: 0.4936 (tmm) REVERT: C 418 ASN cc_start: 0.8290 (m-40) cc_final: 0.8057 (m110) REVERT: D 28 GLU cc_start: 0.8056 (tt0) cc_final: 0.7723 (tm-30) REVERT: D 75 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: D 97 ASP cc_start: 0.8109 (m-30) cc_final: 0.7410 (t0) REVERT: D 113 ASP cc_start: 0.8777 (p0) cc_final: 0.8417 (p0) REVERT: D 126 GLU cc_start: 0.7614 (pm20) cc_final: 0.7101 (mt-10) REVERT: D 156 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.7681 (mmt) REVERT: D 233 GLU cc_start: 0.7626 (tt0) cc_final: 0.7170 (mt-10) REVERT: D 235 GLN cc_start: 0.8550 (mm110) cc_final: 0.8108 (mt0) REVERT: D 398 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6720 (tpp-160) REVERT: E 28 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7732 (tm-30) REVERT: E 49 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8446 (mtmt) REVERT: E 97 ASP cc_start: 0.8109 (m-30) cc_final: 0.7545 (t0) REVERT: E 126 GLU cc_start: 0.7481 (pm20) cc_final: 0.7087 (mt-10) REVERT: E 233 GLU cc_start: 0.7703 (tt0) cc_final: 0.7188 (mt-10) REVERT: E 398 ARG cc_start: 0.7372 (ttm110) cc_final: 0.6588 (tpp-160) outliers start: 79 outliers final: 47 residues processed: 295 average time/residue: 0.5567 time to fit residues: 181.3531 Evaluate side-chains 298 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 395 PHE Chi-restraints excluded: chain A residue 408 VAL 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 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 404 THR 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 170 MET 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 408 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 294 SER 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 283 SER Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 391 MET 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: 4.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 0.0010 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3736 r_free = 0.3736 target = 0.143838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109765 restraints weight = 17457.448| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.04 r_work: 0.3101 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3821 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= 0.129 Angle : 0.641 10.410 19715 Z= 0.319 Chirality : 0.044 0.155 2260 Planarity : 0.003 0.037 2430 Dihedral : 4.885 38.483 1887 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.80 % Allowed : 19.34 % 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: -1.36 (0.19), residues: 1710 helix: -0.36 (0.22), residues: 560 sheet: 0.33 (0.29), residues: 320 loop : -1.80 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 229 TYR 0.017 0.001 TYR D 238 PHE 0.014 0.001 PHE C 258 TRP 0.008 0.001 TRP A 84 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14470) covalent geometry : angle 0.63554 / 0.32 (19650) SS BOND : bond 0.00470 / 0.26 ( 10) SS BOND : angle 2.19277 / 1.08 ( 20) hydrogen bonds : bond 0.03336 / 2.23 ( 533) hydrogen bonds : angle 4.05889 / 2.80 ( 1965) link_BETA1-4 : bond 0.00570 / 0.32 ( 10) link_BETA1-4 : angle 1.42305 / 0.87 ( 30) link_NAG-ASN : bond 0.00207 / 0.11 ( 5) link_NAG-ASN : angle 0.48263 / 0.31 ( 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 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7874 (tt0) cc_final: 0.7516 (tm-30) REVERT: A 36 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8706 (mtpm) REVERT: A 97 ASP cc_start: 0.8073 (m-30) cc_final: 0.7453 (t0) REVERT: A 126 GLU cc_start: 0.7582 (pm20) cc_final: 0.7169 (mt-10) REVERT: A 391 MET cc_start: 0.4350 (OUTLIER) cc_final: 0.3890 (tmm) REVERT: A 398 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6526 (tpp-160) REVERT: B 28 GLU cc_start: 0.8102 (tp30) cc_final: 0.7780 (tm-30) REVERT: B 97 ASP cc_start: 0.8338 (m-30) cc_final: 0.7767 (t0) REVERT: B 126 GLU cc_start: 0.7445 (pm20) cc_final: 0.7041 (mm-30) REVERT: B 171 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: B 233 GLU cc_start: 0.7641 (tt0) cc_final: 0.7135 (mt-10) REVERT: B 308 LEU cc_start: 0.7742 (mp) cc_final: 0.7422 (tt) REVERT: B 398 ARG cc_start: 0.6961 (ttm110) cc_final: 0.6013 (tpp-160) REVERT: C 28 GLU cc_start: 0.8111 (tp30) cc_final: 0.7710 (tm-30) REVERT: C 97 ASP cc_start: 0.8177 (m-30) cc_final: 0.7558 (t0) REVERT: C 126 GLU cc_start: 0.7368 (pm20) cc_final: 0.7021 (mm-30) REVERT: C 189 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8509 (mtpt) REVERT: C 206 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8073 (mttm) REVERT: C 236 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7250 (tmm) REVERT: C 308 LEU cc_start: 0.7855 (mp) cc_final: 0.7601 (tt) REVERT: C 391 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.4979 (tmm) REVERT: D 28 GLU cc_start: 0.8060 (tt0) cc_final: 0.7724 (tm-30) REVERT: D 30 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7680 (mp) REVERT: D 75 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: D 97 ASP cc_start: 0.8099 (m-30) cc_final: 0.7441 (t0) REVERT: D 113 ASP cc_start: 0.8756 (p0) cc_final: 0.8401 (p0) REVERT: D 126 GLU cc_start: 0.7599 (pm20) cc_final: 0.7061 (mt-10) REVERT: D 156 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.7741 (mmt) REVERT: D 207 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8152 (tm-30) REVERT: D 233 GLU cc_start: 0.7621 (tt0) cc_final: 0.7162 (mt-10) REVERT: D 235 GLN cc_start: 0.8542 (mm110) cc_final: 0.8093 (mt0) REVERT: D 308 LEU cc_start: 0.7859 (mp) cc_final: 0.7639 (tt) REVERT: E 28 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7809 (tm-30) REVERT: E 49 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8449 (mtmt) REVERT: E 97 ASP cc_start: 0.8101 (m-30) cc_final: 0.7576 (t0) REVERT: E 126 GLU cc_start: 0.7463 (pm20) cc_final: 0.7049 (mt-10) REVERT: E 308 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7545 (tt) REVERT: E 398 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6537 (tpp-160) outliers start: 73 outliers final: 47 residues processed: 286 average time/residue: 0.5531 time to fit residues: 174.3684 Evaluate side-chains 300 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 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 404 THR Chi-restraints excluded: chain B residue 408 VAL 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 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU 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 30 LEU 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 214 CYS 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 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: 0.3980 chunk 16 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 119 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN D 62 ASN D 131 ASN D 171 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111081 restraints weight = 17415.778| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.04 r_work: 0.3115 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3908 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= 0.120 Angle : 0.635 11.802 19715 Z= 0.316 Chirality : 0.044 0.154 2260 Planarity : 0.003 0.037 2430 Dihedral : 4.801 46.295 1887 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.34 % Allowed : 20.00 % Favored : 75.66 % 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: -1.19 (0.19), residues: 1710 helix: -0.11 (0.22), residues: 560 sheet: 0.38 (0.29), residues: 320 loop : -1.77 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.029 0.001 TYR D 238 PHE 0.014 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 0.00278 / 0.12 (14470) covalent geometry : angle 0.63028 / 0.31 (19650) SS BOND : bond 0.00446 / 0.24 ( 10) SS BOND : angle 1.97095 / 0.99 ( 20) hydrogen bonds : bond 0.03217 / 2.16 ( 533) hydrogen bonds : angle 3.97041 / 2.74 ( 1965) link_BETA1-4 : bond 0.00536 / 0.30 ( 10) link_BETA1-4 : angle 1.41359 / 0.87 ( 30) link_NAG-ASN : bond 0.00217 / 0.13 ( 5) link_NAG-ASN : angle 0.44763 / 0.29 ( 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 321 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7845 (tt0) cc_final: 0.7528 (tm-30) REVERT: A 36 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8710 (mtpm) REVERT: A 97 ASP cc_start: 0.8052 (m-30) cc_final: 0.7406 (t0) REVERT: A 126 GLU cc_start: 0.7609 (pm20) cc_final: 0.7170 (mt-10) REVERT: A 308 LEU cc_start: 0.7704 (mp) cc_final: 0.7446 (tt) REVERT: A 391 MET cc_start: 0.4564 (OUTLIER) cc_final: 0.3886 (tmm) REVERT: A 398 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6550 (tpp-160) REVERT: B 28 GLU cc_start: 0.8100 (tp30) cc_final: 0.7738 (tm-30) REVERT: B 97 ASP cc_start: 0.8299 (m-30) cc_final: 0.7747 (t0) REVERT: B 171 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: B 233 GLU cc_start: 0.7652 (tt0) cc_final: 0.7223 (mt-10) REVERT: B 308 LEU cc_start: 0.7701 (mp) cc_final: 0.7458 (tt) REVERT: B 398 ARG cc_start: 0.6901 (ttm110) cc_final: 0.5927 (tpp-160) REVERT: C 28 GLU cc_start: 0.8040 (tp30) cc_final: 0.7659 (tm-30) REVERT: C 97 ASP cc_start: 0.8197 (m-30) cc_final: 0.7628 (t0) REVERT: C 156 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8284 (mmt) REVERT: C 189 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8513 (mtpt) REVERT: C 206 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8078 (mttm) REVERT: C 308 LEU cc_start: 0.7901 (mp) cc_final: 0.7662 (tt) REVERT: C 391 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4940 (tmm) REVERT: D 28 GLU cc_start: 0.8046 (tt0) cc_final: 0.7752 (tm-30) REVERT: D 30 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7679 (mp) REVERT: D 75 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7693 (ttm-80) REVERT: D 97 ASP cc_start: 0.8072 (m-30) cc_final: 0.7445 (t0) REVERT: D 113 ASP cc_start: 0.8744 (p0) cc_final: 0.8388 (p0) REVERT: D 156 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: D 227 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: D 233 GLU cc_start: 0.7591 (tt0) cc_final: 0.7143 (mt-10) REVERT: D 235 GLN cc_start: 0.8534 (mm110) cc_final: 0.8077 (mt0) REVERT: E 28 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7746 (tm-30) REVERT: E 97 ASP cc_start: 0.8031 (m-30) cc_final: 0.7495 (t0) REVERT: E 163 MET cc_start: 0.8517 (mtm) cc_final: 0.8113 (mpp) REVERT: E 171 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: E 308 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7591 (tt) REVERT: E 398 ARG cc_start: 0.7318 (ttm110) cc_final: 0.6519 (tpp-160) outliers start: 66 outliers final: 44 residues processed: 286 average time/residue: 0.5553 time to fit residues: 175.3919 Evaluate side-chains 294 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 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 130 ASP Chi-restraints excluded: chain C residue 156 MET 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 C residue 408 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 107 ASP 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 227 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 151 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3732 r_free = 0.3732 target = 0.143443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109207 restraints weight = 17548.005| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.05 r_work: 0.3088 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3962 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= 0.150 Angle : 0.671 11.340 19715 Z= 0.333 Chirality : 0.044 0.157 2260 Planarity : 0.003 0.038 2430 Dihedral : 4.848 45.529 1887 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.95 % Allowed : 20.79 % Favored : 75.26 % 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: -1.14 (0.19), residues: 1710 helix: 0.04 (0.23), residues: 565 sheet: 0.40 (0.29), residues: 320 loop : -1.84 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.017 0.001 TYR D 238 PHE 0.014 0.001 PHE C 258 TRP 0.009 0.001 TRP A 259 HIS 0.002 0.000 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14470) covalent geometry : angle 0.66621 / 0.33 (19650) SS BOND : bond 0.00501 / 0.28 ( 10) SS BOND : angle 2.04943 / 1.07 ( 20) hydrogen bonds : bond 0.03318 / 2.23 ( 533) hydrogen bonds : angle 4.03793 / 2.79 ( 1965) link_BETA1-4 : bond 0.00583 / 0.33 ( 10) link_BETA1-4 : angle 1.42083 / 0.87 ( 30) link_NAG-ASN : bond 0.00151 / 0.09 ( 5) link_NAG-ASN : angle 0.45668 / 0.30 ( 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 302 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7805 (tt0) cc_final: 0.7522 (tm-30) REVERT: A 36 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8722 (mtpm) REVERT: A 97 ASP cc_start: 0.8000 (m-30) cc_final: 0.7355 (t0) REVERT: A 126 GLU cc_start: 0.7592 (pm20) cc_final: 0.7118 (mt-10) REVERT: A 308 LEU cc_start: 0.7703 (mp) cc_final: 0.7451 (tt) REVERT: A 391 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.4009 (tmm) REVERT: A 398 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6542 (tpp-160) REVERT: B 28 GLU cc_start: 0.8067 (tp30) cc_final: 0.7702 (tm-30) REVERT: B 97 ASP cc_start: 0.8292 (m-30) cc_final: 0.7737 (t0) REVERT: B 126 GLU cc_start: 0.7669 (pm20) cc_final: 0.7220 (mm-30) REVERT: B 171 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: B 233 GLU cc_start: 0.7778 (tt0) cc_final: 0.7263 (mt-10) REVERT: B 308 LEU cc_start: 0.7735 (mp) cc_final: 0.7486 (tt) REVERT: B 398 ARG cc_start: 0.6910 (ttm110) cc_final: 0.5913 (tpp-160) REVERT: C 28 GLU cc_start: 0.8069 (tp30) cc_final: 0.7664 (tm-30) REVERT: C 97 ASP cc_start: 0.8178 (m-30) cc_final: 0.7631 (t0) REVERT: C 189 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (mtpt) REVERT: C 206 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8052 (mttm) REVERT: C 225 CYS cc_start: 0.7218 (t) cc_final: 0.6927 (t) REVERT: C 391 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.4966 (tmm) REVERT: D 28 GLU cc_start: 0.8073 (tt0) cc_final: 0.7771 (tm-30) REVERT: D 30 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7658 (mp) REVERT: D 75 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: D 97 ASP cc_start: 0.8048 (m-30) cc_final: 0.7465 (t0) REVERT: D 113 ASP cc_start: 0.8768 (p0) cc_final: 0.8405 (p0) REVERT: D 126 GLU cc_start: 0.7605 (pm20) cc_final: 0.7101 (mt-10) REVERT: D 156 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7678 (mmt) REVERT: D 207 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8110 (tm-30) REVERT: D 227 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: D 233 GLU cc_start: 0.7616 (tt0) cc_final: 0.7170 (mt-10) REVERT: E 28 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7810 (tm-30) REVERT: E 97 ASP cc_start: 0.8092 (m-30) cc_final: 0.7592 (t0) REVERT: E 126 GLU cc_start: 0.7563 (pm20) cc_final: 0.7167 (mm-30) REVERT: E 189 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8372 (mtpt) REVERT: E 206 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8452 (mttp) REVERT: E 308 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7512 (tt) REVERT: E 398 ARG cc_start: 0.7320 (ttm110) cc_final: 0.6491 (tpp-160) outliers start: 60 outliers final: 45 residues processed: 277 average time/residue: 0.5546 time to fit residues: 169.7248 Evaluate side-chains 295 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 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 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 30 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 107 ASP 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 227 GLU Chi-restraints excluded: chain D residue 294 SER 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 189 LYS Chi-restraints excluded: chain E residue 214 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 138 optimal weight: 0.0000 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3729 r_free = 0.3729 target = 0.143659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111275 restraints weight = 17184.142| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.91 r_work: 0.3129 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14495 Z= 0.120 Angle : 0.657 12.464 19715 Z= 0.326 Chirality : 0.044 0.156 2260 Planarity : 0.003 0.036 2430 Dihedral : 4.744 46.235 1887 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.62 % Allowed : 21.12 % Favored : 75.26 % 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: -1.01 (0.20), residues: 1710 helix: 0.23 (0.23), residues: 565 sheet: 0.44 (0.29), residues: 320 loop : -1.81 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.033 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 E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (14470) covalent geometry : angle 0.65324 / 0.33 (19650) SS BOND : bond 0.00414 / 0.23 ( 10) SS BOND : angle 1.83772 / 0.93 ( 20) hydrogen bonds : bond 0.03262 / 2.21 ( 533) hydrogen bonds : angle 3.91896 / 2.70 ( 1965) link_BETA1-4 : bond 0.00518 / 0.29 ( 10) link_BETA1-4 : angle 1.42110 / 0.87 ( 30) link_NAG-ASN : bond 0.00213 / 0.12 ( 5) link_NAG-ASN : angle 0.40921 / 0.27 ( 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 284 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7807 (tt0) cc_final: 0.7543 (tm-30) REVERT: A 36 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8712 (mtpp) REVERT: A 97 ASP cc_start: 0.7981 (m-30) cc_final: 0.7372 (t0) REVERT: A 308 LEU cc_start: 0.7701 (mp) cc_final: 0.7486 (tt) REVERT: A 391 MET cc_start: 0.4634 (OUTLIER) cc_final: 0.3980 (tmm) REVERT: A 398 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6501 (tpp-160) REVERT: B 28 GLU cc_start: 0.8075 (tp30) cc_final: 0.7734 (tm-30) REVERT: B 97 ASP cc_start: 0.8254 (m-30) cc_final: 0.7739 (t0) REVERT: B 126 GLU cc_start: 0.7604 (pm20) cc_final: 0.7100 (mt-10) REVERT: B 171 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: B 227 GLU cc_start: 0.8792 (pt0) cc_final: 0.8463 (pt0) REVERT: B 308 LEU cc_start: 0.7716 (mp) cc_final: 0.7496 (tt) REVERT: B 398 ARG cc_start: 0.6864 (ttm110) cc_final: 0.5885 (tpp-160) REVERT: C 28 GLU cc_start: 0.8026 (tp30) cc_final: 0.7603 (tm-30) REVERT: C 97 ASP cc_start: 0.8122 (m-30) cc_final: 0.7599 (t0) REVERT: C 126 GLU cc_start: 0.7391 (pm20) cc_final: 0.6981 (mm-30) REVERT: C 189 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8499 (mtpt) REVERT: C 206 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8033 (mttm) REVERT: C 225 CYS cc_start: 0.7170 (t) cc_final: 0.6913 (t) REVERT: C 227 GLU cc_start: 0.8761 (pt0) cc_final: 0.8347 (tt0) REVERT: C 391 MET cc_start: 0.5252 (OUTLIER) cc_final: 0.4928 (tmm) REVERT: D 28 GLU cc_start: 0.8068 (tt0) cc_final: 0.7769 (tm-30) REVERT: D 75 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7577 (ttm-80) REVERT: D 97 ASP cc_start: 0.8023 (m-30) cc_final: 0.7454 (t0) REVERT: D 113 ASP cc_start: 0.8732 (p0) cc_final: 0.8367 (p0) REVERT: D 126 GLU cc_start: 0.7570 (pm20) cc_final: 0.7060 (mt-10) REVERT: D 207 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8192 (tm-30) REVERT: D 227 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: E 97 ASP cc_start: 0.8012 (m-30) cc_final: 0.7515 (t0) REVERT: E 163 MET cc_start: 0.8500 (mtm) cc_final: 0.8107 (mpp) REVERT: E 171 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: E 206 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8460 (mttp) REVERT: E 398 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6406 (tpp-160) outliers start: 55 outliers final: 41 residues processed: 264 average time/residue: 0.5316 time to fit residues: 155.4392 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 : 0.460 ------------------------------------------------------------------------------- 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 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 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 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 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 107 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 408 VAL 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 283 SER Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 408 VAL 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: 2.9990 chunk 136 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 chunk 116 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3756 r_free = 0.3756 target = 0.145587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111491 restraints weight = 17370.262| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.04 r_work: 0.3121 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 0.071 14495 Z= 0.124 Angle : 0.659 12.144 19715 Z= 0.327 Chirality : 0.044 0.155 2260 Planarity : 0.003 0.036 2430 Dihedral : 4.704 45.127 1887 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.09 % Allowed : 21.78 % Favored : 75.13 % 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: -0.93 (0.20), residues: 1710 helix: 0.29 (0.23), residues: 575 sheet: 0.51 (0.30), residues: 320 loop : -1.79 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.015 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 0.00295 / 0.12 (14470) covalent geometry : angle 0.65497 / 0.33 (19650) SS BOND : bond 0.00429 / 0.23 ( 10) SS BOND : angle 1.89808 / 0.98 ( 20) hydrogen bonds : bond 0.03205 / 2.19 ( 533) hydrogen bonds : angle 3.91052 / 2.71 ( 1965) link_BETA1-4 : bond 0.00494 / 0.29 ( 10) link_BETA1-4 : angle 1.39219 / 0.85 ( 30) link_NAG-ASN : bond 0.00172 / 0.10 ( 5) link_NAG-ASN : angle 0.44036 / 0.29 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.73 seconds wall clock time: 77 minutes 31.21 seconds (4651.21 seconds total)