Starting phenix.real_space_refine on Wed Mar 4 13:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm5_20388/03_2026/6pm5_20388.map" } resolution = 3.1 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= 0.065 sd= 3.206 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9120 2.51 5 N 2275 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13975 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.33, per 1000 atoms: 0.17 Number of scatterers: 13975 At special positions: 0 Unit cell: (106.167, 106.167, 134.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2480 8.00 N 2275 7.00 C 9120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 557.5 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 40.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.542A 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 107 removed outlier: 3.642A pdb=" N ASP A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.719A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.534A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.542A 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 107 removed outlier: 3.641A pdb=" N ASP B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.609A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.719A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.542A 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 107 removed outlier: 3.643A pdb=" N ASP C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.773A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.505A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.611A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.720A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.542A 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 107 removed outlier: 3.642A pdb=" N ASP D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.718A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE D 428 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.542A 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 107 removed outlier: 3.642A pdb=" N ASP E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 428 removed outlier: 3.609A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.719A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 428 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.272A 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: 3.727A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.567A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.681A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 645 hydrogen bonds defined for protein. 1935 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: 2.14 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4285 1.34 - 1.46: 3522 1.46 - 1.58: 6343 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14320 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 19024 1.33 - 2.67: 302 2.67 - 4.00: 69 4.00 - 5.33: 45 5.33 - 6.67: 10 Bond angle restraints: 19450 Sorted by residual: angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.74 6.21 3.00e+00 1.11e-01 4.29e+00 angle pdb=" C3 BMA I 3 " pdb=" C2 BMA I 3 " pdb=" O2 BMA I 3 " ideal model delta sigma weight residual 112.95 106.76 6.19 3.00e+00 1.11e-01 4.26e+00 angle pdb=" C3 BMA J 3 " pdb=" C2 BMA J 3 " pdb=" O2 BMA J 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.25e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.78 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.79 6.16 3.00e+00 1.11e-01 4.22e+00 ... (remaining 19445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 8540 21.72 - 43.44: 120 43.44 - 65.16: 0 65.16 - 86.88: 30 86.88 - 108.60: 20 Dihedral angle restraints: 8710 sinusoidal: 3595 harmonic: 5115 Sorted by residual: dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.89 108.60 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.87 108.58 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.86 108.57 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 2245 0.197 - 0.393: 5 0.393 - 0.590: 0 0.590 - 0.787: 0 0.787 - 0.984: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 ... (remaining 2252 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO E 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO C 411 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.017 5.00e-02 4.00e+02 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3735 2.80 - 3.33: 12281 3.33 - 3.85: 21877 3.85 - 4.38: 26629 4.38 - 4.90: 45304 Nonbonded interactions: 109826 Sorted by model distance: nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.276 3.040 ... (remaining 109821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.003 0.066 14340 Z= 0.134 Angle : 1.002 40.291 19505 Z= 0.376 Chirality : 0.063 0.984 2255 Planarity : 0.003 0.031 2400 Dihedral : 11.101 108.604 5375 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.15), residues: 1710 helix: -3.74 (0.12), residues: 535 sheet: -2.45 (0.21), residues: 380 loop : -2.45 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 135 TYR 0.004 0.000 TYR D 74 PHE 0.003 0.001 PHE A 203 TRP 0.003 0.000 TRP D 422 HIS 0.001 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00194 (14320) covalent geometry : angle 0.48996 (19450) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.95347 ( 10) hydrogen bonds : bond 0.29720 ( 550) hydrogen bonds : angle 9.94095 ( 1935) link_BETA1-4 : bond 0.06488 ( 10) link_BETA1-4 : angle 22.27907 ( 30) link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 0.65402 ( 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 354 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.6039 (mmp) cc_final: 0.5671 (ppp) REVERT: A 185 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 210 ASP cc_start: 0.7649 (m-30) cc_final: 0.7280 (m-30) REVERT: A 303 MET cc_start: 0.8856 (mmt) cc_final: 0.8599 (mmt) REVERT: A 398 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6366 (mmp80) REVERT: B 105 MET cc_start: 0.6130 (mmp) cc_final: 0.5608 (ppp) REVERT: B 210 ASP cc_start: 0.7667 (m-30) cc_final: 0.7249 (m-30) REVERT: B 303 MET cc_start: 0.8915 (mmt) cc_final: 0.8556 (mmt) REVERT: B 390 GLU cc_start: 0.5402 (mp0) cc_final: 0.4918 (mp0) REVERT: B 398 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6380 (mmp80) REVERT: C 105 MET cc_start: 0.6194 (mmp) cc_final: 0.5614 (ppp) REVERT: C 185 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 210 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (m-30) REVERT: C 398 ARG cc_start: 0.7401 (ttm170) cc_final: 0.6614 (mmp80) REVERT: D 105 MET cc_start: 0.5942 (mmp) cc_final: 0.5610 (ppp) REVERT: D 106 LEU cc_start: 0.7783 (tm) cc_final: 0.7406 (tp) REVERT: D 163 MET cc_start: 0.7048 (mpp) cc_final: 0.6787 (mpp) REVERT: D 210 ASP cc_start: 0.7557 (m-30) cc_final: 0.7068 (m-30) REVERT: D 398 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6811 (mmp80) REVERT: E 185 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 210 ASP cc_start: 0.7581 (m-30) cc_final: 0.7153 (m-30) REVERT: E 303 MET cc_start: 0.8951 (mmt) cc_final: 0.8744 (mmt) REVERT: E 398 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6551 (mmp80) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1301 time to fit residues: 64.8212 Evaluate side-chains 263 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 166 GLN A 193 GLN A 235 GLN B 82 GLN B 141 ASN B 166 GLN B 321 ASN C 141 ASN C 166 GLN C 193 GLN D 82 GLN D 139 ASN D 166 GLN D 235 GLN E 82 GLN E 139 ASN E 166 GLN E 180 ASN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113783 restraints weight = 17275.041| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.99 r_work: 0.3111 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14340 Z= 0.144 Angle : 0.651 7.272 19505 Z= 0.317 Chirality : 0.045 0.135 2255 Planarity : 0.004 0.046 2400 Dihedral : 8.455 60.158 2190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.64 % Allowed : 9.36 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.18), residues: 1710 helix: -1.60 (0.18), residues: 610 sheet: -1.48 (0.24), residues: 380 loop : -2.32 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 229 TYR 0.016 0.001 TYR C 238 PHE 0.009 0.001 PHE D 115 TRP 0.008 0.001 TRP E 84 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00317 (14320) covalent geometry : angle 0.62649 (19450) SS BOND : bond 0.00117 ( 5) SS BOND : angle 1.07378 ( 10) hydrogen bonds : bond 0.05612 ( 550) hydrogen bonds : angle 5.58993 ( 1935) link_BETA1-4 : bond 0.00728 ( 10) link_BETA1-4 : angle 4.26284 ( 30) link_NAG-ASN : bond 0.01411 ( 5) link_NAG-ASN : angle 2.17740 ( 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 377 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8210 (t0) cc_final: 0.7927 (t0) REVERT: A 180 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (p0) REVERT: A 398 ARG cc_start: 0.6906 (ttm170) cc_final: 0.5796 (mmp80) REVERT: B 41 ASP cc_start: 0.8135 (t0) cc_final: 0.7894 (t0) REVERT: B 91 TYR cc_start: 0.8277 (p90) cc_final: 0.7719 (p90) REVERT: B 163 MET cc_start: 0.7552 (mpp) cc_final: 0.6682 (mpp) REVERT: B 210 ASP cc_start: 0.7763 (m-30) cc_final: 0.7124 (m-30) REVERT: B 229 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7544 (mtp85) REVERT: B 398 ARG cc_start: 0.6996 (ttm170) cc_final: 0.5895 (mmp80) REVERT: C 41 ASP cc_start: 0.8232 (t0) cc_final: 0.8002 (t0) REVERT: C 185 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 398 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6245 (mmp80) REVERT: D 229 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7679 (mtp85) REVERT: D 398 ARG cc_start: 0.7200 (ttm170) cc_final: 0.6354 (mmp80) REVERT: E 41 ASP cc_start: 0.8169 (t0) cc_final: 0.7949 (t0) REVERT: E 163 MET cc_start: 0.7509 (mpp) cc_final: 0.6554 (mpp) REVERT: E 185 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7883 (mt-10) REVERT: E 210 ASP cc_start: 0.7640 (m-30) cc_final: 0.7189 (m-30) REVERT: E 229 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7671 (mtp85) REVERT: E 303 MET cc_start: 0.8482 (mmt) cc_final: 0.8084 (mmt) REVERT: E 398 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6112 (mmp80) outliers start: 39 outliers final: 25 residues processed: 360 average time/residue: 0.1220 time to fit residues: 61.9944 Evaluate side-chains 306 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 321 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 321 ASN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118327 restraints weight = 17460.605| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.72 r_work: 0.3252 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14340 Z= 0.121 Angle : 0.612 7.403 19505 Z= 0.292 Chirality : 0.044 0.147 2255 Planarity : 0.004 0.040 2400 Dihedral : 5.923 35.345 2190 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.85 % Allowed : 11.05 % Favored : 86.10 % 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: -1.88 (0.19), residues: 1710 helix: -0.45 (0.21), residues: 610 sheet: -0.79 (0.26), residues: 380 loop : -2.16 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 229 TYR 0.013 0.001 TYR B 317 PHE 0.012 0.001 PHE E 311 TRP 0.008 0.001 TRP A 422 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00277 (14320) covalent geometry : angle 0.59438 (19450) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.95665 ( 10) hydrogen bonds : bond 0.04187 ( 550) hydrogen bonds : angle 4.75262 ( 1935) link_BETA1-4 : bond 0.00471 ( 10) link_BETA1-4 : angle 3.74685 ( 30) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 0.77852 ( 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 335 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8533 (t0) cc_final: 0.8273 (t0) REVERT: A 163 MET cc_start: 0.7655 (mpp) cc_final: 0.6639 (mpp) REVERT: A 177 TYR cc_start: 0.8843 (m-80) cc_final: 0.8443 (m-80) REVERT: A 180 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 193 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: A 398 ARG cc_start: 0.7142 (ttm170) cc_final: 0.6035 (mmp80) REVERT: B 91 TYR cc_start: 0.8672 (p90) cc_final: 0.8234 (p90) REVERT: B 163 MET cc_start: 0.7432 (mpp) cc_final: 0.6997 (mpp) REVERT: B 210 ASP cc_start: 0.8081 (m-30) cc_final: 0.7621 (m-30) REVERT: B 229 ARG cc_start: 0.8391 (mtp85) cc_final: 0.8109 (mtp85) REVERT: B 398 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6089 (mmp80) REVERT: C 41 ASP cc_start: 0.8618 (t0) cc_final: 0.8413 (t0) REVERT: C 177 TYR cc_start: 0.8835 (m-80) cc_final: 0.8501 (m-80) REVERT: C 185 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8015 (mt-10) REVERT: C 398 ARG cc_start: 0.7208 (ttm170) cc_final: 0.6367 (mmp80) REVERT: D 141 ASN cc_start: 0.8812 (m-40) cc_final: 0.8507 (m-40) REVERT: D 177 TYR cc_start: 0.8827 (m-80) cc_final: 0.8593 (m-80) REVERT: D 398 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6517 (mmp80) REVERT: E 91 TYR cc_start: 0.8482 (p90) cc_final: 0.7918 (p90) REVERT: E 173 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: E 177 TYR cc_start: 0.8861 (m-80) cc_final: 0.8495 (m-80) REVERT: E 185 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8100 (mt-10) REVERT: E 398 ARG cc_start: 0.7333 (ttm170) cc_final: 0.6426 (mmp80) outliers start: 42 outliers final: 27 residues processed: 323 average time/residue: 0.1064 time to fit residues: 50.7286 Evaluate side-chains 294 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN D 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113939 restraints weight = 17592.838| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.79 r_work: 0.3172 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14340 Z= 0.152 Angle : 0.621 8.084 19505 Z= 0.302 Chirality : 0.045 0.173 2255 Planarity : 0.004 0.043 2400 Dihedral : 4.906 30.334 2190 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.73 % Allowed : 12.68 % Favored : 83.59 % 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: -1.32 (0.20), residues: 1710 helix: 0.15 (0.22), residues: 610 sheet: -0.20 (0.27), residues: 345 loop : -2.08 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 229 TYR 0.017 0.002 TYR B 144 PHE 0.010 0.001 PHE C 124 TRP 0.007 0.001 TRP B 84 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00361 (14320) covalent geometry : angle 0.60312 (19450) SS BOND : bond 0.00351 ( 5) SS BOND : angle 2.25091 ( 10) hydrogen bonds : bond 0.03719 ( 550) hydrogen bonds : angle 4.49595 ( 1935) link_BETA1-4 : bond 0.00490 ( 10) link_BETA1-4 : angle 3.59415 ( 30) link_NAG-ASN : bond 0.00413 ( 5) link_NAG-ASN : angle 0.83631 ( 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 344 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 0.482 Fit side-chains REVERT: A 163 MET cc_start: 0.7813 (mpp) cc_final: 0.7170 (mpp) REVERT: A 180 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8282 (p0) REVERT: A 398 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6060 (mmp80) REVERT: B 91 TYR cc_start: 0.8897 (p90) cc_final: 0.8494 (p90) REVERT: B 104 SER cc_start: 0.8236 (m) cc_final: 0.7994 (p) REVERT: B 177 TYR cc_start: 0.8908 (m-80) cc_final: 0.8598 (m-80) REVERT: B 225 CYS cc_start: 0.6929 (t) cc_final: 0.6703 (t) REVERT: B 398 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6093 (mmp80) REVERT: C 225 CYS cc_start: 0.7120 (t) cc_final: 0.6784 (t) REVERT: C 314 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6782 (tt) REVERT: C 398 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6326 (mmp80) REVERT: D 91 TYR cc_start: 0.8967 (p90) cc_final: 0.8695 (p90) REVERT: D 177 TYR cc_start: 0.8896 (m-80) cc_final: 0.8582 (m-80) REVERT: D 398 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6502 (mmp80) REVERT: E 105 MET cc_start: 0.7254 (ppp) cc_final: 0.6619 (ppp) REVERT: E 173 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: E 177 TYR cc_start: 0.8929 (m-80) cc_final: 0.8701 (m-80) REVERT: E 398 ARG cc_start: 0.7290 (ttm170) cc_final: 0.6392 (mmp80) outliers start: 55 outliers final: 42 residues processed: 316 average time/residue: 0.1048 time to fit residues: 49.6686 Evaluate side-chains 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN D 180 ASN D 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111292 restraints weight = 17612.608| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.76 r_work: 0.3163 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14340 Z= 0.132 Angle : 0.605 7.639 19505 Z= 0.293 Chirality : 0.044 0.166 2255 Planarity : 0.003 0.043 2400 Dihedral : 4.695 29.876 2190 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.39 % Allowed : 14.78 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1710 helix: 0.49 (0.22), residues: 610 sheet: -0.02 (0.28), residues: 350 loop : -1.91 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.017 0.001 TYR D 317 PHE 0.009 0.001 PHE B 115 TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00316 (14320) covalent geometry : angle 0.58648 (19450) SS BOND : bond 0.00368 ( 5) SS BOND : angle 2.63909 ( 10) hydrogen bonds : bond 0.03467 ( 550) hydrogen bonds : angle 4.35683 ( 1935) link_BETA1-4 : bond 0.00495 ( 10) link_BETA1-4 : angle 3.46932 ( 30) link_NAG-ASN : bond 0.00343 ( 5) link_NAG-ASN : angle 0.78348 ( 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 338 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7746 (mpp) cc_final: 0.7211 (mpp) REVERT: A 180 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8284 (p0) REVERT: A 398 ARG cc_start: 0.7121 (ttm170) cc_final: 0.6137 (mmp80) REVERT: B 91 TYR cc_start: 0.8898 (p90) cc_final: 0.8517 (p90) REVERT: B 104 SER cc_start: 0.8357 (m) cc_final: 0.8093 (p) REVERT: B 177 TYR cc_start: 0.8929 (m-80) cc_final: 0.8563 (m-80) REVERT: B 398 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6133 (mmp80) REVERT: C 93 GLU cc_start: 0.7324 (pm20) cc_final: 0.6937 (pm20) REVERT: C 104 SER cc_start: 0.8437 (m) cc_final: 0.8197 (p) REVERT: C 314 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6767 (tt) REVERT: C 398 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6369 (mmp80) REVERT: D 91 TYR cc_start: 0.8975 (p90) cc_final: 0.8646 (p90) REVERT: D 177 TYR cc_start: 0.8914 (m-80) cc_final: 0.8673 (m-80) REVERT: D 398 ARG cc_start: 0.7317 (ttm170) cc_final: 0.6520 (mmp80) REVERT: E 105 MET cc_start: 0.7297 (ppp) cc_final: 0.6664 (ppp) REVERT: E 173 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: E 177 TYR cc_start: 0.8954 (m-80) cc_final: 0.8736 (m-80) REVERT: E 398 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6418 (mmp80) outliers start: 50 outliers final: 38 residues processed: 313 average time/residue: 0.0974 time to fit residues: 46.2899 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 0.0040 chunk 127 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN D 180 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114766 restraints weight = 17503.591| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.83 r_work: 0.3174 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14340 Z= 0.110 Angle : 0.589 9.742 19505 Z= 0.284 Chirality : 0.043 0.168 2255 Planarity : 0.003 0.042 2400 Dihedral : 4.560 44.778 2190 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.53 % Allowed : 16.68 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.63 (0.21), residues: 1710 helix: 0.75 (0.23), residues: 610 sheet: 0.30 (0.28), residues: 350 loop : -1.79 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 229 TYR 0.016 0.001 TYR A 317 PHE 0.009 0.001 PHE B 115 TRP 0.008 0.001 TRP E 84 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00257 (14320) covalent geometry : angle 0.56916 (19450) SS BOND : bond 0.00255 ( 5) SS BOND : angle 3.61572 ( 10) hydrogen bonds : bond 0.03229 ( 550) hydrogen bonds : angle 4.19603 ( 1935) link_BETA1-4 : bond 0.00527 ( 10) link_BETA1-4 : angle 3.32260 ( 30) link_NAG-ASN : bond 0.00318 ( 5) link_NAG-ASN : angle 0.76971 ( 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 332 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7728 (t70) cc_final: 0.7472 (t70) REVERT: A 163 MET cc_start: 0.7729 (mpp) cc_final: 0.7400 (mpp) REVERT: A 180 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 398 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6063 (mmp80) REVERT: B 177 TYR cc_start: 0.8920 (m-80) cc_final: 0.8541 (m-80) REVERT: B 398 ARG cc_start: 0.7199 (ttm170) cc_final: 0.6131 (mmp80) REVERT: C 314 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6802 (tt) REVERT: C 398 ARG cc_start: 0.7185 (ttm170) cc_final: 0.6335 (mmp80) REVERT: D 91 TYR cc_start: 0.8978 (p90) cc_final: 0.8640 (p90) REVERT: D 173 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: D 177 TYR cc_start: 0.8939 (m-80) cc_final: 0.8716 (m-80) REVERT: D 225 CYS cc_start: 0.7209 (t) cc_final: 0.6772 (t) REVERT: D 398 ARG cc_start: 0.7324 (ttm170) cc_final: 0.6508 (mmp80) REVERT: E 105 MET cc_start: 0.7209 (ppp) cc_final: 0.6440 (ppp) REVERT: E 173 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: E 398 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6442 (mmp80) outliers start: 52 outliers final: 44 residues processed: 304 average time/residue: 0.1013 time to fit residues: 46.1462 Evaluate side-chains 316 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN B 141 ASN C 219 ASN D 180 ASN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112170 restraints weight = 17530.249| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.76 r_work: 0.3177 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14340 Z= 0.113 Angle : 0.597 9.475 19505 Z= 0.287 Chirality : 0.043 0.170 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.486 43.638 2190 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.46 % Allowed : 17.29 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.47 (0.21), residues: 1710 helix: 0.86 (0.23), residues: 610 sheet: 0.51 (0.29), residues: 340 loop : -1.71 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.016 0.001 TYR A 317 PHE 0.009 0.001 PHE B 115 TRP 0.007 0.001 TRP A 84 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00264 (14320) covalent geometry : angle 0.57697 (19450) SS BOND : bond 0.00318 ( 5) SS BOND : angle 3.78097 ( 10) hydrogen bonds : bond 0.03129 ( 550) hydrogen bonds : angle 4.13807 ( 1935) link_BETA1-4 : bond 0.00514 ( 10) link_BETA1-4 : angle 3.25867 ( 30) link_NAG-ASN : bond 0.00292 ( 5) link_NAG-ASN : angle 0.78877 ( 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 326 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7754 (t70) cc_final: 0.7490 (t70) REVERT: A 180 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 398 ARG cc_start: 0.7060 (ttm170) cc_final: 0.6066 (mmp80) REVERT: B 173 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: B 177 TYR cc_start: 0.8931 (m-80) cc_final: 0.8551 (m-80) REVERT: B 398 ARG cc_start: 0.7197 (ttm170) cc_final: 0.6139 (mmp80) REVERT: C 102 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7619 (t70) REVERT: C 139 ASN cc_start: 0.9208 (p0) cc_final: 0.9004 (p0) REVERT: C 189 LYS cc_start: 0.7916 (mptt) cc_final: 0.7707 (mptt) REVERT: C 398 ARG cc_start: 0.7170 (ttm170) cc_final: 0.6338 (mmp80) REVERT: D 91 TYR cc_start: 0.8983 (p90) cc_final: 0.8664 (p90) REVERT: D 102 ASP cc_start: 0.7666 (t70) cc_final: 0.7418 (t70) REVERT: D 173 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: D 177 TYR cc_start: 0.8954 (m-80) cc_final: 0.8714 (m-80) REVERT: D 398 ARG cc_start: 0.7324 (ttm170) cc_final: 0.6523 (mmp80) REVERT: E 105 MET cc_start: 0.7179 (ppp) cc_final: 0.6438 (ppp) REVERT: E 236 MET cc_start: 0.8032 (mmm) cc_final: 0.7285 (mmm) REVERT: E 398 ARG cc_start: 0.7287 (ttm170) cc_final: 0.6456 (mmp80) outliers start: 51 outliers final: 41 residues processed: 302 average time/residue: 0.1022 time to fit residues: 46.4951 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 168 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109657 restraints weight = 17601.551| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.76 r_work: 0.3146 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14340 Z= 0.142 Angle : 0.640 10.049 19505 Z= 0.312 Chirality : 0.044 0.172 2255 Planarity : 0.003 0.040 2400 Dihedral : 4.816 54.975 2190 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.46 % Allowed : 17.29 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.42 (0.21), residues: 1710 helix: 0.86 (0.23), residues: 610 sheet: 0.55 (0.29), residues: 340 loop : -1.66 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.017 0.002 TYR D 317 PHE 0.010 0.001 PHE B 311 TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00341 (14320) covalent geometry : angle 0.61646 (19450) SS BOND : bond 0.00571 ( 5) SS BOND : angle 5.27574 ( 10) hydrogen bonds : bond 0.03210 ( 550) hydrogen bonds : angle 4.23651 ( 1935) link_BETA1-4 : bond 0.00535 ( 10) link_BETA1-4 : angle 3.22543 ( 30) link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 0.90492 ( 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 324 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7813 (t70) cc_final: 0.7568 (t70) REVERT: A 180 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8305 (p0) REVERT: A 398 ARG cc_start: 0.7085 (ttm170) cc_final: 0.6104 (mmp80) REVERT: B 177 TYR cc_start: 0.8961 (m-80) cc_final: 0.8586 (m-80) REVERT: B 398 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6166 (mmp80) REVERT: C 102 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7705 (t70) REVERT: C 139 ASN cc_start: 0.9221 (p0) cc_final: 0.8985 (p0) REVERT: C 398 ARG cc_start: 0.7173 (ttm170) cc_final: 0.6388 (mmp80) REVERT: D 91 TYR cc_start: 0.9014 (p90) cc_final: 0.8716 (p90) REVERT: D 102 ASP cc_start: 0.7712 (t70) cc_final: 0.7490 (t70) REVERT: D 173 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: D 177 TYR cc_start: 0.8972 (m-80) cc_final: 0.8724 (m-80) REVERT: D 398 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6521 (mmp80) REVERT: D 401 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6810 (ttm-80) REVERT: E 105 MET cc_start: 0.7247 (ppp) cc_final: 0.6506 (ppp) REVERT: E 173 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: E 236 MET cc_start: 0.8030 (mmm) cc_final: 0.7353 (mmm) REVERT: E 398 ARG cc_start: 0.7302 (ttm170) cc_final: 0.6467 (mmp80) outliers start: 51 outliers final: 45 residues processed: 297 average time/residue: 0.1012 time to fit residues: 45.3451 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 132 optimal weight: 0.0670 chunk 159 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112119 restraints weight = 17520.987| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.73 r_work: 0.3149 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14340 Z= 0.131 Angle : 0.643 9.990 19505 Z= 0.313 Chirality : 0.044 0.173 2255 Planarity : 0.003 0.038 2400 Dihedral : 4.872 54.727 2190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.46 % Allowed : 17.42 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1710 helix: 0.92 (0.23), residues: 610 sheet: 0.55 (0.29), residues: 340 loop : -1.60 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 229 TYR 0.016 0.002 TYR D 317 PHE 0.011 0.001 PHE C 311 TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00314 (14320) covalent geometry : angle 0.61914 (19450) SS BOND : bond 0.00369 ( 5) SS BOND : angle 5.34024 ( 10) hydrogen bonds : bond 0.03123 ( 550) hydrogen bonds : angle 4.20937 ( 1935) link_BETA1-4 : bond 0.00527 ( 10) link_BETA1-4 : angle 3.18436 ( 30) link_NAG-ASN : bond 0.00259 ( 5) link_NAG-ASN : angle 0.87416 ( 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 320 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7859 (t70) cc_final: 0.7621 (t70) REVERT: A 180 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8286 (p0) REVERT: A 398 ARG cc_start: 0.7081 (ttm170) cc_final: 0.6114 (mmp80) REVERT: B 173 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: B 177 TYR cc_start: 0.8962 (m-80) cc_final: 0.8596 (m-80) REVERT: B 398 ARG cc_start: 0.7179 (ttm170) cc_final: 0.6165 (mmp80) REVERT: C 102 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7761 (t70) REVERT: C 139 ASN cc_start: 0.9221 (p0) cc_final: 0.8998 (p0) REVERT: C 253 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7191 (mp) REVERT: C 398 ARG cc_start: 0.7225 (ttm170) cc_final: 0.6501 (mmp80) REVERT: D 91 TYR cc_start: 0.8997 (p90) cc_final: 0.8755 (p90) REVERT: D 102 ASP cc_start: 0.7790 (t70) cc_final: 0.7587 (t70) REVERT: D 173 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: D 177 TYR cc_start: 0.8981 (m-80) cc_final: 0.8732 (m-80) REVERT: D 398 ARG cc_start: 0.7334 (ttm170) cc_final: 0.6534 (mmp80) REVERT: D 401 ARG cc_start: 0.7220 (tpt170) cc_final: 0.6816 (ttm-80) REVERT: E 28 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6913 (tm-30) REVERT: E 105 MET cc_start: 0.7268 (ppp) cc_final: 0.6464 (ppp) REVERT: E 173 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: E 236 MET cc_start: 0.8007 (mmm) cc_final: 0.7278 (mmm) REVERT: E 279 MET cc_start: 0.9048 (mmm) cc_final: 0.8737 (tpt) REVERT: E 398 ARG cc_start: 0.7299 (ttm170) cc_final: 0.6463 (mmp80) outliers start: 51 outliers final: 36 residues processed: 296 average time/residue: 0.0999 time to fit residues: 44.5772 Evaluate side-chains 304 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112880 restraints weight = 17501.280| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.73 r_work: 0.3158 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14340 Z= 0.123 Angle : 0.643 9.558 19505 Z= 0.311 Chirality : 0.044 0.174 2255 Planarity : 0.003 0.038 2400 Dihedral : 4.866 56.493 2190 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.05 % Allowed : 17.76 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1710 helix: 1.01 (0.23), residues: 610 sheet: 0.57 (0.29), residues: 340 loop : -1.56 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 229 TYR 0.016 0.001 TYR C 317 PHE 0.010 0.001 PHE A 311 TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00293 (14320) covalent geometry : angle 0.62053 (19450) SS BOND : bond 0.00329 ( 5) SS BOND : angle 5.27102 ( 10) hydrogen bonds : bond 0.03057 ( 550) hydrogen bonds : angle 4.16675 ( 1935) link_BETA1-4 : bond 0.00532 ( 10) link_BETA1-4 : angle 3.12295 ( 30) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 0.87656 ( 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 312 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7881 (t70) cc_final: 0.7658 (t70) REVERT: A 180 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8276 (p0) REVERT: A 398 ARG cc_start: 0.7079 (ttm170) cc_final: 0.6108 (mmp80) REVERT: B 173 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: B 177 TYR cc_start: 0.8935 (m-80) cc_final: 0.8561 (m-80) REVERT: B 398 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6195 (mmp80) REVERT: C 102 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7792 (t70) REVERT: C 398 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6487 (mmp80) REVERT: D 173 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 177 TYR cc_start: 0.8977 (m-80) cc_final: 0.8730 (m-80) REVERT: D 398 ARG cc_start: 0.7320 (ttm170) cc_final: 0.6570 (mmp80) REVERT: D 401 ARG cc_start: 0.7214 (tpt170) cc_final: 0.6810 (ttm-80) REVERT: E 28 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6850 (tm-30) REVERT: E 105 MET cc_start: 0.7280 (ppp) cc_final: 0.6504 (ppp) REVERT: E 173 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: E 236 MET cc_start: 0.7903 (mmm) cc_final: 0.7665 (mmm) REVERT: E 279 MET cc_start: 0.9030 (mmm) cc_final: 0.8778 (tpt) REVERT: E 398 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6454 (mmp80) outliers start: 45 outliers final: 37 residues processed: 290 average time/residue: 0.1028 time to fit residues: 45.0430 Evaluate side-chains 298 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 171 GLN D 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115563 restraints weight = 17453.779| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.69 r_work: 0.3160 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14340 Z= 0.131 Angle : 0.653 9.798 19505 Z= 0.316 Chirality : 0.044 0.175 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.869 55.852 2190 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.25 % Allowed : 17.83 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1710 helix: 1.04 (0.22), residues: 610 sheet: 0.58 (0.29), residues: 340 loop : -1.50 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 229 TYR 0.017 0.002 TYR D 317 PHE 0.012 0.001 PHE C 311 TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00315 (14320) covalent geometry : angle 0.63055 (19450) SS BOND : bond 0.00391 ( 5) SS BOND : angle 5.38457 ( 10) hydrogen bonds : bond 0.03055 ( 550) hydrogen bonds : angle 4.19197 ( 1935) link_BETA1-4 : bond 0.00527 ( 10) link_BETA1-4 : angle 3.09257 ( 30) link_NAG-ASN : bond 0.00234 ( 5) link_NAG-ASN : angle 0.89722 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.40 seconds wall clock time: 48 minutes 33.84 seconds (2913.84 seconds total)