Starting phenix.real_space_refine on Sat Sep 12 05:51:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm5_20388/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm5_20388/09_2026/6pm5_20388.cif" } 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-2.2.1-6174/lib/python3.11/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 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: 2.42, 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: 1.14 Conformation dependent library (CDL) restraints added in 498.1 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: 0.34 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: 2.07 Time building geometry restraints manager: 1.52 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 - 8.63: 7748 8.63 - 17.26: 462 17.26 - 25.89: 135 25.89 - 34.52: 25 34.52 - 43.16: 35 Dihedral angle restraints: 8405 sinusoidal: 3290 harmonic: 5115 Sorted by residual: dihedral pdb=" CA LEU C 182 " pdb=" CB LEU C 182 " pdb=" CG LEU C 182 " pdb=" CD1 LEU C 182 " ideal model delta sinusoidal sigma weight residual 180.00 136.84 43.16 3 1.50e+01 4.44e-03 7.75e+00 dihedral pdb=" CA LEU D 182 " pdb=" CB LEU D 182 " pdb=" CG LEU D 182 " pdb=" CD1 LEU D 182 " ideal model delta sinusoidal sigma weight residual 180.00 136.88 43.12 3 1.50e+01 4.44e-03 7.75e+00 dihedral pdb=" CA LEU E 182 " pdb=" CB LEU E 182 " pdb=" CG LEU E 182 " pdb=" CD1 LEU E 182 " ideal model delta sinusoidal sigma weight residual 180.00 136.89 43.11 3 1.50e+01 4.44e-03 7.75e+00 ... (remaining 8402 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: 0.02 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: 1.880 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 6.821 43.156 5070 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/Z covalent geometry : bond 0.00194 / 0.10 (14320) covalent geometry : angle 0.48996 / 0.24 (19450) SS BOND : bond 0.00133 / 0.08 ( 5) SS BOND : angle 0.95347 / 0.54 ( 10) hydrogen bonds : bond 0.29720 / 19.78 ( 550) hydrogen bonds : angle 9.94095 / 6.73 ( 1935) link_BETA1-4 : bond 0.06488 / 3.84 ( 10) link_BETA1-4 : angle 22.27907 / 16.56 ( 30) link_NAG-ASN : bond 0.00125 / 0.07 ( 5) link_NAG-ASN : angle 0.65402 / 0.36 ( 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 : 0.538 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: 0.1275 time to fit residues: 63.6239 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 : 0.349 ------------------------------------------------------------------------------- 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... A 82 GLN A 166 GLN A 193 GLN A 235 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113589 restraints weight = 17275.006| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.00 r_work: 0.3110 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2306 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 : 0.635 7.260 19505 Z= 0.318 Chirality : 0.045 0.138 2255 Planarity : 0.004 0.047 2400 Dihedral : 3.604 14.829 1885 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.64 % Allowed : 9.29 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.18), residues: 1710 helix: -1.46 (0.19), residues: 610 sheet: -1.37 (0.24), residues: 380 loop : -2.31 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 229 TYR 0.020 0.001 TYR C 238 PHE 0.009 0.001 PHE E 48 TRP 0.009 0.001 TRP E 84 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14320) covalent geometry : angle 0.62352 / 0.32 (19450) SS BOND : bond 0.00098 / 0.06 ( 5) SS BOND : angle 1.08918 / 0.65 ( 10) hydrogen bonds : bond 0.04866 / 3.23 ( 550) hydrogen bonds : angle 5.42540 / 3.69 ( 1935) link_BETA1-4 : bond 0.01092 / 0.61 ( 10) link_BETA1-4 : angle 3.01586 / 2.07 ( 30) link_NAG-ASN : bond 0.00107 / 0.06 ( 5) link_NAG-ASN : angle 1.10571 / 0.65 ( 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 380 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8227 (t0) cc_final: 0.7941 (t0) REVERT: A 180 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8117 (p0) REVERT: A 398 ARG cc_start: 0.6893 (ttm170) cc_final: 0.5768 (mmp80) REVERT: B 41 ASP cc_start: 0.8127 (t0) cc_final: 0.7856 (t0) REVERT: B 91 TYR cc_start: 0.8287 (p90) cc_final: 0.7731 (p90) REVERT: B 141 ASN cc_start: 0.8169 (m-40) cc_final: 0.7877 (m-40) REVERT: B 163 MET cc_start: 0.7544 (mpp) cc_final: 0.6676 (mpp) REVERT: B 210 ASP cc_start: 0.7761 (m-30) cc_final: 0.7137 (m-30) REVERT: B 229 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7536 (mtp85) REVERT: B 398 ARG cc_start: 0.6969 (ttm170) cc_final: 0.5865 (mmp80) REVERT: C 41 ASP cc_start: 0.8268 (t0) cc_final: 0.8057 (t0) REVERT: C 173 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 185 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 398 ARG cc_start: 0.7146 (ttm170) cc_final: 0.6223 (mmp80) REVERT: D 163 MET cc_start: 0.7436 (mpp) cc_final: 0.6554 (mpp) REVERT: D 229 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7654 (mtp85) REVERT: D 398 ARG cc_start: 0.7193 (ttm170) cc_final: 0.6353 (mmp80) REVERT: E 41 ASP cc_start: 0.8200 (t0) cc_final: 0.7993 (t0) REVERT: E 105 MET cc_start: 0.6750 (ppp) cc_final: 0.5883 (ppp) REVERT: E 163 MET cc_start: 0.7496 (mpp) cc_final: 0.6582 (mpp) REVERT: E 185 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7882 (mt-10) REVERT: E 210 ASP cc_start: 0.7622 (m-30) cc_final: 0.7203 (m-30) REVERT: E 229 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7659 (mtp85) REVERT: E 303 MET cc_start: 0.8417 (mmt) cc_final: 0.8015 (mmt) REVERT: E 398 ARG cc_start: 0.7101 (ttm170) cc_final: 0.6111 (mmp80) outliers start: 39 outliers final: 25 residues processed: 363 average time/residue: 0.1195 time to fit residues: 61.6845 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 7 optimal weight: 0.0000 chunk 16 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN B 82 GLN C 82 GLN D 219 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 = 0.3708 r_free = 0.3708 target = 0.148279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122653 restraints weight = 17443.052| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.79 r_work: 0.3275 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14340 Z= 0.106 Angle : 0.581 7.053 19505 Z= 0.281 Chirality : 0.043 0.122 2255 Planarity : 0.003 0.040 2400 Dihedral : 3.564 18.538 1885 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.92 % Allowed : 11.25 % Favored : 85.83 % 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: -1.85 (0.19), residues: 1710 helix: -0.37 (0.21), residues: 610 sheet: -0.48 (0.27), residues: 345 loop : -2.32 (0.19), residues: 755 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 D 422 HIS 0.001 0.000 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14320) covalent geometry : angle 0.57107 / 0.28 (19450) SS BOND : bond 0.00160 / 0.10 ( 5) SS BOND : angle 0.93521 / 0.56 ( 10) hydrogen bonds : bond 0.04153 / 2.73 ( 550) hydrogen bonds : angle 4.72163 / 3.23 ( 1935) link_BETA1-4 : bond 0.00585 / 0.36 ( 10) link_BETA1-4 : angle 2.80024 / 1.92 ( 30) link_NAG-ASN : bond 0.00401 / 0.23 ( 5) link_NAG-ASN : angle 0.44868 / 0.26 ( 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 343 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8508 (t0) cc_final: 0.8248 (t0) REVERT: A 163 MET cc_start: 0.7668 (mpp) cc_final: 0.6597 (mpp) REVERT: A 177 TYR cc_start: 0.8816 (m-80) cc_final: 0.8413 (m-80) REVERT: A 180 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 193 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: A 398 ARG cc_start: 0.7157 (ttm170) cc_final: 0.5979 (mmp80) REVERT: B 91 TYR cc_start: 0.8605 (p90) cc_final: 0.8195 (p90) REVERT: B 141 ASN cc_start: 0.8659 (m-40) cc_final: 0.8366 (m-40) REVERT: B 163 MET cc_start: 0.7395 (mpp) cc_final: 0.6901 (mpp) REVERT: B 210 ASP cc_start: 0.8080 (m-30) cc_final: 0.7626 (m-30) REVERT: B 229 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8129 (mtp85) REVERT: B 398 ARG cc_start: 0.7177 (ttm170) cc_final: 0.6072 (mmp80) REVERT: C 41 ASP cc_start: 0.8597 (t0) cc_final: 0.8394 (t0) REVERT: C 177 TYR cc_start: 0.8831 (m-80) cc_final: 0.8499 (m-80) REVERT: C 185 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8019 (mt-10) REVERT: C 398 ARG cc_start: 0.7229 (ttm170) cc_final: 0.6379 (mmp80) REVERT: D 91 TYR cc_start: 0.8609 (p90) cc_final: 0.8162 (p90) REVERT: D 141 ASN cc_start: 0.8793 (m-40) cc_final: 0.8487 (m-40) REVERT: D 177 TYR cc_start: 0.8802 (m-80) cc_final: 0.8528 (m-80) REVERT: D 398 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6474 (mmp80) REVERT: E 91 TYR cc_start: 0.8429 (p90) cc_final: 0.7888 (p90) REVERT: E 177 TYR cc_start: 0.8832 (m-80) cc_final: 0.8446 (m-80) REVERT: E 185 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8122 (mt-10) REVERT: E 398 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6375 (mmp80) outliers start: 43 outliers final: 26 residues processed: 331 average time/residue: 0.1029 time to fit residues: 50.9432 Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 214 CYS 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 214 CYS 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 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN 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 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN B 82 GLN 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 = 0.3654 r_free = 0.3654 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117214 restraints weight = 17492.212| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.77 r_work: 0.3211 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14340 Z= 0.132 Angle : 0.589 8.953 19505 Z= 0.287 Chirality : 0.043 0.176 2255 Planarity : 0.004 0.041 2400 Dihedral : 3.783 28.223 1885 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.12 % Allowed : 12.95 % Favored : 83.93 % 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: -1.34 (0.20), residues: 1710 helix: 0.19 (0.22), residues: 610 sheet: -0.33 (0.26), residues: 370 loop : -2.13 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 229 TYR 0.015 0.001 TYR B 144 PHE 0.009 0.001 PHE B 311 TRP 0.007 0.001 TRP B 84 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14320) covalent geometry : angle 0.57840 / 0.28 (19450) SS BOND : bond 0.00296 / 0.18 ( 5) SS BOND : angle 1.85451 / 1.16 ( 10) hydrogen bonds : bond 0.03652 / 2.38 ( 550) hydrogen bonds : angle 4.44012 / 3.04 ( 1935) link_BETA1-4 : bond 0.00533 / 0.32 ( 10) link_BETA1-4 : angle 2.75255 / 1.87 ( 30) link_NAG-ASN : bond 0.00348 / 0.20 ( 5) link_NAG-ASN : angle 0.56444 / 0.31 ( 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 336 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.8693 (p90) cc_final: 0.8124 (p90) REVERT: A 163 MET cc_start: 0.7725 (mpp) cc_final: 0.6867 (mpp) REVERT: A 180 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8298 (p0) REVERT: A 398 ARG cc_start: 0.7108 (ttm170) cc_final: 0.6010 (mmp80) REVERT: B 91 TYR cc_start: 0.8816 (p90) cc_final: 0.8402 (p90) REVERT: B 104 SER cc_start: 0.8446 (m) cc_final: 0.8215 (p) REVERT: B 163 MET cc_start: 0.7658 (mpp) cc_final: 0.7048 (mpp) REVERT: B 177 TYR cc_start: 0.8869 (m-80) cc_final: 0.8568 (m-80) REVERT: B 210 ASP cc_start: 0.7982 (m-30) cc_final: 0.7609 (m-30) REVERT: B 398 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6061 (mmp80) REVERT: C 177 TYR cc_start: 0.8937 (m-80) cc_final: 0.8733 (m-80) REVERT: C 398 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6299 (mmp80) REVERT: D 177 TYR cc_start: 0.8824 (m-80) cc_final: 0.8454 (m-80) REVERT: D 398 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6454 (mmp80) REVERT: E 105 MET cc_start: 0.7231 (ppp) cc_final: 0.6556 (ppp) REVERT: E 177 TYR cc_start: 0.8910 (m-80) cc_final: 0.8672 (m-80) REVERT: E 185 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8038 (mt-10) REVERT: E 236 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7069 (tmm) REVERT: E 398 ARG cc_start: 0.7286 (ttm170) cc_final: 0.6389 (mmp80) outliers start: 46 outliers final: 32 residues processed: 312 average time/residue: 0.1150 time to fit residues: 53.6884 Evaluate side-chains 305 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 214 CYS 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 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 253 LEU 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 127 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 219 ASN C 321 ASN D 180 ASN ** D 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 = 0.3614 r_free = 0.3614 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113280 restraints weight = 17320.950| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.74 r_work: 0.3128 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14340 Z= 0.174 Angle : 0.631 7.910 19505 Z= 0.313 Chirality : 0.045 0.143 2255 Planarity : 0.004 0.047 2400 Dihedral : 4.254 35.421 1885 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 3.86 % Allowed : 13.90 % Favored : 82.24 % 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: -0.98 (0.20), residues: 1710 helix: 0.49 (0.22), residues: 610 sheet: -0.08 (0.28), residues: 350 loop : -1.92 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 229 TYR 0.019 0.002 TYR B 144 PHE 0.012 0.002 PHE B 124 TRP 0.007 0.001 TRP C 302 HIS 0.005 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (14320) covalent geometry : angle 0.61882 / 0.31 (19450) SS BOND : bond 0.01162 / 0.58 ( 5) SS BOND : angle 2.83849 / 1.39 ( 10) hydrogen bonds : bond 0.03585 / 2.33 ( 550) hydrogen bonds : angle 4.43210 / 3.03 ( 1935) link_BETA1-4 : bond 0.00570 / 0.34 ( 10) link_BETA1-4 : angle 2.75224 / 1.87 ( 30) link_NAG-ASN : bond 0.00379 / 0.22 ( 5) link_NAG-ASN : angle 0.78770 / 0.43 ( 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 339 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.7857 (mpp) cc_final: 0.7481 (mpp) REVERT: A 180 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 398 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6040 (mmp80) REVERT: B 91 TYR cc_start: 0.9005 (p90) cc_final: 0.8607 (p90) REVERT: B 398 ARG cc_start: 0.7243 (ttm170) cc_final: 0.6161 (mmp80) REVERT: C 104 SER cc_start: 0.8485 (m) cc_final: 0.8282 (p) REVERT: C 177 TYR cc_start: 0.8988 (m-80) cc_final: 0.8731 (m-80) REVERT: C 225 CYS cc_start: 0.7201 (t) cc_final: 0.6956 (t) REVERT: C 398 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6453 (mmp80) REVERT: D 177 TYR cc_start: 0.8946 (m-80) cc_final: 0.8741 (m-80) REVERT: D 225 CYS cc_start: 0.7307 (t) cc_final: 0.7026 (t) REVERT: D 398 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6515 (mmp80) REVERT: D 401 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6812 (ttm-80) REVERT: E 105 MET cc_start: 0.7308 (ppp) cc_final: 0.6621 (ppp) REVERT: E 177 TYR cc_start: 0.8989 (m-80) cc_final: 0.8715 (m-80) REVERT: E 398 ARG cc_start: 0.7360 (ttm170) cc_final: 0.6485 (mmp80) outliers start: 57 outliers final: 48 residues processed: 310 average time/residue: 0.1116 time to fit residues: 52.1028 Evaluate side-chains 321 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 323 ILE 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 214 CYS Chi-restraints excluded: chain B residue 216 LYS 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 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 405 VAL 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 253 LEU 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 179 MET Chi-restraints excluded: chain E residue 216 LYS 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 Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 109 optimal weight: 50.0000 chunk 43 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 ASN D 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115989 restraints weight = 17220.072| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.74 r_work: 0.3158 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3889 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= 0.114 Angle : 0.595 11.488 19505 Z= 0.290 Chirality : 0.043 0.142 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.195 45.847 1885 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.12 % Allowed : 17.29 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1710 helix: 0.75 (0.23), residues: 610 sheet: 0.26 (0.28), residues: 350 loop : -1.76 (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 0.010 0.001 PHE C 115 TRP 0.008 0.001 TRP E 422 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (14320) covalent geometry : angle 0.57858 / 0.28 (19450) SS BOND : bond 0.00441 / 0.25 ( 5) SS BOND : angle 4.15071 / 2.29 ( 10) hydrogen bonds : bond 0.03274 / 2.12 ( 550) hydrogen bonds : angle 4.19885 / 2.88 ( 1935) link_BETA1-4 : bond 0.00551 / 0.34 ( 10) link_BETA1-4 : angle 2.70116 / 1.83 ( 30) link_NAG-ASN : bond 0.00282 / 0.17 ( 5) link_NAG-ASN : angle 0.56272 / 0.30 ( 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 330 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 284 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7754 (t70) cc_final: 0.7498 (t70) REVERT: A 180 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8274 (p0) REVERT: A 398 ARG cc_start: 0.7077 (ttm170) cc_final: 0.6064 (mmp80) REVERT: B 91 TYR cc_start: 0.8932 (p90) cc_final: 0.8716 (p90) REVERT: B 177 TYR cc_start: 0.8941 (m-80) cc_final: 0.8545 (m-80) REVERT: B 219 ASN cc_start: 0.8238 (p0) cc_final: 0.7952 (p0) REVERT: B 398 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6141 (mmp80) REVERT: C 102 ASP cc_start: 0.7845 (t70) cc_final: 0.7562 (t70) REVERT: C 104 SER cc_start: 0.8616 (m) cc_final: 0.8412 (p) REVERT: C 139 ASN cc_start: 0.9187 (p0) cc_final: 0.8974 (p0) REVERT: C 177 TYR cc_start: 0.8975 (m-80) cc_final: 0.8755 (m-80) REVERT: C 225 CYS cc_start: 0.7224 (t) cc_final: 0.6972 (t) REVERT: C 398 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6393 (mmp80) REVERT: D 177 TYR cc_start: 0.8955 (m-80) cc_final: 0.8743 (m-80) REVERT: D 398 ARG cc_start: 0.7300 (ttm170) cc_final: 0.6507 (mmp80) REVERT: D 401 ARG cc_start: 0.7174 (tpt170) cc_final: 0.6813 (ttm-80) REVERT: E 105 MET cc_start: 0.7258 (ppp) cc_final: 0.6540 (ppp) REVERT: E 177 TYR cc_start: 0.8993 (m-80) cc_final: 0.8759 (m-80) REVERT: E 398 ARG cc_start: 0.7300 (ttm170) cc_final: 0.6467 (mmp80) outliers start: 46 outliers final: 35 residues processed: 306 average time/residue: 0.1143 time to fit residues: 52.4318 Evaluate side-chains 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 214 CYS 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 241 ILE 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 254 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 129 THR Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET 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: 4.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112306 restraints weight = 17487.101| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.82 r_work: 0.3149 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4023 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= 0.123 Angle : 0.604 10.393 19505 Z= 0.294 Chirality : 0.043 0.146 2255 Planarity : 0.003 0.038 2400 Dihedral : 4.178 46.643 1885 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.32 % Allowed : 17.15 % Favored : 79.53 % 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: -0.43 (0.21), residues: 1710 helix: 0.89 (0.23), residues: 610 sheet: 0.39 (0.28), residues: 350 loop : -1.64 (0.22), 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 0.011 0.001 PHE C 115 TRP 0.009 0.001 TRP E 422 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14320) covalent geometry : angle 0.58854 / 0.29 (19450) SS BOND : bond 0.00302 / 0.19 ( 5) SS BOND : angle 4.04920 / 2.19 ( 10) hydrogen bonds : bond 0.03213 / 2.08 ( 550) hydrogen bonds : angle 4.15848 / 2.85 ( 1935) link_BETA1-4 : bond 0.00535 / 0.32 ( 10) link_BETA1-4 : angle 2.65250 / 1.80 ( 30) link_NAG-ASN : bond 0.00252 / 0.15 ( 5) link_NAG-ASN : angle 0.64869 / 0.35 ( 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 330 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7824 (t70) cc_final: 0.7575 (t70) REVERT: A 180 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 398 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6089 (mmp80) REVERT: B 177 TYR cc_start: 0.8942 (m-80) cc_final: 0.8525 (m-80) REVERT: B 235 GLN cc_start: 0.8664 (mm110) cc_final: 0.8231 (mm-40) REVERT: B 398 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6161 (mmp80) REVERT: C 93 GLU cc_start: 0.7385 (pm20) cc_final: 0.6928 (pm20) REVERT: C 102 ASP cc_start: 0.7931 (t70) cc_final: 0.7635 (t70) REVERT: C 139 ASN cc_start: 0.9213 (p0) cc_final: 0.8997 (p0) REVERT: C 177 TYR cc_start: 0.8961 (m-80) cc_final: 0.8729 (m-80) REVERT: C 225 CYS cc_start: 0.7224 (t) cc_final: 0.6973 (t) REVERT: C 398 ARG cc_start: 0.7158 (ttm170) cc_final: 0.6372 (mmp80) REVERT: D 177 TYR cc_start: 0.8961 (m-80) cc_final: 0.8737 (m-80) REVERT: D 398 ARG cc_start: 0.7300 (ttm170) cc_final: 0.6504 (mmp80) REVERT: D 401 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6793 (ttm-80) REVERT: E 105 MET cc_start: 0.7267 (ppp) cc_final: 0.6483 (ppp) REVERT: E 177 TYR cc_start: 0.8994 (m-80) cc_final: 0.8728 (m-80) REVERT: E 398 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6451 (mmp80) outliers start: 49 outliers final: 38 residues processed: 303 average time/residue: 0.0987 time to fit residues: 45.4907 Evaluate side-chains 307 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 214 CYS 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 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 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET 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 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU 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: 2.9990 chunk 125 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 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 = 0.3584 r_free = 0.3584 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110758 restraints weight = 17482.534| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.79 r_work: 0.3132 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4181 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= 0.136 Angle : 0.614 9.529 19505 Z= 0.299 Chirality : 0.044 0.147 2255 Planarity : 0.003 0.041 2400 Dihedral : 4.254 46.509 1885 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.46 % Allowed : 17.08 % Favored : 79.46 % 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: -0.35 (0.21), residues: 1710 helix: 0.93 (0.23), residues: 610 sheet: 0.40 (0.29), residues: 350 loop : -1.55 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.018 0.002 TYR C 317 PHE 0.011 0.001 PHE C 115 TRP 0.007 0.001 TRP B 186 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14320) covalent geometry : angle 0.60013 / 0.29 (19450) SS BOND : bond 0.00414 / 0.24 ( 5) SS BOND : angle 3.72775 / 2.03 ( 10) hydrogen bonds : bond 0.03187 / 2.08 ( 550) hydrogen bonds : angle 4.18684 / 2.87 ( 1935) link_BETA1-4 : bond 0.00535 / 0.32 ( 10) link_BETA1-4 : angle 2.62093 / 1.77 ( 30) link_NAG-ASN : bond 0.00222 / 0.13 ( 5) link_NAG-ASN : angle 0.70962 / 0.38 ( 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 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7851 (t70) cc_final: 0.7621 (t70) REVERT: A 180 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (p0) REVERT: A 398 ARG cc_start: 0.7075 (ttm170) cc_final: 0.6091 (mmp80) REVERT: B 177 TYR cc_start: 0.8952 (m-80) cc_final: 0.8519 (m-80) REVERT: B 398 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6207 (mmp80) REVERT: C 102 ASP cc_start: 0.7976 (t70) cc_final: 0.7710 (t70) REVERT: C 177 TYR cc_start: 0.8959 (m-80) cc_final: 0.8700 (m-80) REVERT: C 253 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7183 (mp) REVERT: C 398 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6424 (mmp80) REVERT: D 177 TYR cc_start: 0.8997 (m-80) cc_final: 0.8761 (m-80) REVERT: D 398 ARG cc_start: 0.7314 (ttm170) cc_final: 0.6551 (mmp80) REVERT: D 401 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6794 (ttm-80) REVERT: E 105 MET cc_start: 0.7261 (ppp) cc_final: 0.6467 (ppp) REVERT: E 177 TYR cc_start: 0.8975 (m-80) cc_final: 0.8693 (m-80) REVERT: E 309 PHE cc_start: 0.7715 (m-80) cc_final: 0.7448 (m-80) REVERT: E 398 ARG cc_start: 0.7288 (ttm170) cc_final: 0.6451 (mmp80) outliers start: 51 outliers final: 42 residues processed: 297 average time/residue: 0.1067 time to fit residues: 47.9776 Evaluate side-chains 307 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 LYS 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 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 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 214 CYS 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 165 VAL Chi-restraints excluded: chain C residue 220 THR 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 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 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU 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: 2.9990 chunk 117 optimal weight: 3.9990 chunk 132 optimal weight: 0.0060 chunk 159 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 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 = 0.3590 r_free = 0.3590 target = 0.137615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111469 restraints weight = 17446.872| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.77 r_work: 0.3142 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14340 Z= 0.122 Angle : 0.611 9.291 19505 Z= 0.296 Chirality : 0.043 0.149 2255 Planarity : 0.003 0.037 2400 Dihedral : 4.334 46.766 1885 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.12 % Allowed : 17.22 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1710 helix: 1.01 (0.22), residues: 610 sheet: 0.43 (0.28), residues: 350 loop : -1.49 (0.22), residues: 750 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 A 186 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (14320) covalent geometry : angle 0.59589 / 0.29 (19450) SS BOND : bond 0.00317 / 0.19 ( 5) SS BOND : angle 4.15372 / 2.14 ( 10) hydrogen bonds : bond 0.03095 / 2.01 ( 550) hydrogen bonds : angle 4.15884 / 2.84 ( 1935) link_BETA1-4 : bond 0.00542 / 0.33 ( 10) link_BETA1-4 : angle 2.60581 / 1.76 ( 30) link_NAG-ASN : bond 0.00218 / 0.13 ( 5) link_NAG-ASN : angle 0.67653 / 0.37 ( 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 315 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7855 (t70) cc_final: 0.7627 (t70) REVERT: A 180 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 398 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6092 (mmp80) REVERT: B 177 TYR cc_start: 0.8940 (m-80) cc_final: 0.8507 (m-80) REVERT: B 235 GLN cc_start: 0.8635 (mm110) cc_final: 0.8262 (mm-40) REVERT: B 398 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6217 (mmp80) REVERT: C 102 ASP cc_start: 0.7996 (t70) cc_final: 0.7742 (t70) REVERT: C 177 TYR cc_start: 0.8939 (m-80) cc_final: 0.8684 (m-80) REVERT: C 398 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6466 (mmp80) REVERT: D 177 TYR cc_start: 0.8986 (m-80) cc_final: 0.8751 (m-80) REVERT: D 398 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6554 (mmp80) REVERT: D 401 ARG cc_start: 0.7185 (tpt170) cc_final: 0.6793 (ttm-80) REVERT: E 105 MET cc_start: 0.7229 (ppp) cc_final: 0.6393 (ppp) REVERT: E 177 TYR cc_start: 0.8974 (m-80) cc_final: 0.8695 (m-80) REVERT: E 253 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7028 (mp) REVERT: E 309 PHE cc_start: 0.7716 (m-80) cc_final: 0.7442 (m-80) REVERT: E 398 ARG cc_start: 0.7286 (ttm170) cc_final: 0.6452 (mmp80) outliers start: 46 outliers final: 39 residues processed: 293 average time/residue: 0.1076 time to fit residues: 47.4932 Evaluate side-chains 305 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 214 CYS 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 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 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 E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 253 LEU 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: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110299 restraints weight = 17523.753| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.78 r_work: 0.3121 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14340 Z= 0.144 Angle : 0.629 9.221 19505 Z= 0.306 Chirality : 0.044 0.148 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.414 46.757 1885 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.98 % Allowed : 17.49 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1710 helix: 0.95 (0.22), residues: 615 sheet: 0.44 (0.28), residues: 350 loop : -1.41 (0.23), residues: 745 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 0.011 0.001 PHE C 311 TRP 0.006 0.001 TRP A 186 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (14320) covalent geometry : angle 0.61376 / 0.30 (19450) SS BOND : bond 0.00338 / 0.21 ( 5) SS BOND : angle 4.25502 / 2.16 ( 10) hydrogen bonds : bond 0.03131 / 2.04 ( 550) hydrogen bonds : angle 4.20237 / 2.87 ( 1935) link_BETA1-4 : bond 0.00527 / 0.32 ( 10) link_BETA1-4 : angle 2.58904 / 1.75 ( 30) link_NAG-ASN : bond 0.00185 / 0.11 ( 5) link_NAG-ASN : angle 0.74932 / 0.41 ( 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 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7890 (t70) cc_final: 0.7676 (t70) REVERT: A 180 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8282 (p0) REVERT: A 398 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6115 (mmp80) REVERT: B 177 TYR cc_start: 0.8950 (m-80) cc_final: 0.8504 (m-80) REVERT: B 235 GLN cc_start: 0.8650 (mm110) cc_final: 0.8263 (mm-40) REVERT: B 398 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6219 (mmp80) REVERT: C 102 ASP cc_start: 0.7985 (t70) cc_final: 0.7750 (t70) REVERT: C 177 TYR cc_start: 0.8945 (m-80) cc_final: 0.8678 (m-80) REVERT: C 398 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6532 (mmp80) REVERT: D 177 TYR cc_start: 0.8993 (m-80) cc_final: 0.8746 (m-80) REVERT: D 398 ARG cc_start: 0.7327 (ttm170) cc_final: 0.6592 (mmp80) REVERT: D 401 ARG cc_start: 0.7205 (tpt170) cc_final: 0.6811 (ttm-80) REVERT: E 105 MET cc_start: 0.7286 (ppp) cc_final: 0.7066 (ppp) REVERT: E 177 TYR cc_start: 0.8985 (m-80) cc_final: 0.8673 (m-80) REVERT: E 253 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7040 (mp) REVERT: E 309 PHE cc_start: 0.7740 (m-80) cc_final: 0.7531 (m-80) REVERT: E 398 ARG cc_start: 0.7296 (ttm170) cc_final: 0.6457 (mmp80) outliers start: 44 outliers final: 40 residues processed: 290 average time/residue: 0.1128 time to fit residues: 49.2778 Evaluate side-chains 305 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 LYS 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 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 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 214 CYS 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 165 VAL 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 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 254 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 129 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 253 LEU 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: 0.0770 chunk 160 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114108 restraints weight = 17353.039| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.80 r_work: 0.3134 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14340 Z= 0.129 Angle : 0.627 8.882 19505 Z= 0.304 Chirality : 0.044 0.151 2255 Planarity : 0.003 0.041 2400 Dihedral : 4.408 45.856 1885 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.98 % Allowed : 18.17 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1710 helix: 1.01 (0.22), residues: 615 sheet: 0.56 (0.28), residues: 345 loop : -1.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 229 TYR 0.017 0.001 TYR A 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/Z covalent geometry : bond 0.00310 / 0.13 (14320) covalent geometry : angle 0.61250 / 0.30 (19450) SS BOND : bond 0.00285 / 0.18 ( 5) SS BOND : angle 4.08443 / 2.08 ( 10) hydrogen bonds : bond 0.03080 / 2.00 ( 550) hydrogen bonds : angle 4.15735 / 2.84 ( 1935) link_BETA1-4 : bond 0.00530 / 0.32 ( 10) link_BETA1-4 : angle 2.57571 / 1.74 ( 30) link_NAG-ASN : bond 0.00182 / 0.11 ( 5) link_NAG-ASN : angle 0.74061 / 0.40 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.15 seconds wall clock time: 51 minutes 10.74 seconds (3070.74 seconds total)