Starting phenix.real_space_refine on Thu Jul 2 21:13:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2026/7u2t_26319.map" } resolution = 3.25 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= 0.007 sd= 0.158 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 88 5.16 5 C 6524 2.51 5 N 1728 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10300 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 1.61, per 1000 atoms: 0.16 Number of scatterers: 10300 At special positions: 0 Unit cell: (117.16, 117.16, 63.8, 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 88 16.00 O 1960 8.00 N 1728 7.00 C 6524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.07 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.07 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.07 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.07 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.05 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.05 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.05 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 NAG-ASN " NAG A 501 " - " ASN A 235 " " NAG A 502 " - " ASN A 88 " " NAG B 501 " - " ASN B 235 " " NAG B 502 " - " ASN B 88 " " NAG C 501 " - " ASN C 235 " " NAG C 502 " - " ASN C 88 " " NAG D 501 " - " ASN D 235 " " NAG D 502 " - " ASN D 88 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 264.9 milliseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.9% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER A 444 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU A 259 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS A 279 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 291 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS A 281 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 289 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER B 444 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU B 259 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 291 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS B 281 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 289 " --> pdb=" O CYS B 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER C 444 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU C 259 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS C 279 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 291 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS C 281 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 289 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.047A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY D 395 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 936 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: 1.36 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2811 1.33 - 1.47: 2977 1.47 - 1.60: 4648 1.60 - 1.73: 0 1.73 - 1.86: 112 Bond restraints: 10548 Sorted by residual: bond pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU D 119 " pdb=" CA GLU D 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N CYS D 281 " pdb=" CA CYS D 281 " ideal model delta sigma weight residual 1.454 1.498 -0.043 1.23e-02 6.61e+03 1.25e+01 ... (remaining 10543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11694 1.83 - 3.66: 2109 3.66 - 5.49: 373 5.49 - 7.32: 95 7.32 - 9.15: 25 Bond angle restraints: 14296 Sorted by residual: angle pdb=" C GLY B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY D 197 " pdb=" N PRO D 198 " pdb=" CA PRO D 198 " ideal model delta sigma weight residual 119.78 128.90 -9.12 1.03e+00 9.43e-01 7.84e+01 angle pdb=" C SER D 153 " pdb=" N PRO D 154 " pdb=" CA PRO D 154 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.65e+01 ... (remaining 14291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 5848 15.12 - 30.24: 236 30.24 - 45.35: 52 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 6180 sinusoidal: 2416 harmonic: 3764 Sorted by residual: dihedral pdb=" C TYR B 402 " pdb=" N TYR B 402 " pdb=" CA TYR B 402 " pdb=" CB TYR B 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR D 402 " pdb=" N TYR D 402 " pdb=" CA TYR D 402 " pdb=" CB TYR D 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR C 402 " pdb=" N TYR C 402 " pdb=" CA TYR C 402 " pdb=" CB TYR C 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 920 0.071 - 0.142: 467 0.142 - 0.214: 121 0.214 - 0.285: 48 0.285 - 0.356: 16 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 1569 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG C 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.024 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5428 2.99 - 3.47: 8951 3.47 - 3.94: 17493 3.94 - 4.42: 20235 4.42 - 4.90: 33594 Nonbonded interactions: 85701 Sorted by model distance: nonbonded pdb=" N ASP A 416 " pdb=" OD1 ASP A 416 " model vdw 2.512 3.120 nonbonded pdb=" N ASP B 416 " pdb=" OD1 ASP B 416 " model vdw 2.512 3.120 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.512 3.120 nonbonded pdb=" N ASP D 416 " pdb=" OD1 ASP D 416 " model vdw 2.513 3.120 nonbonded pdb=" N GLN C 136 " pdb=" N GLY C 137 " model vdw 2.518 2.560 ... (remaining 85696 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' } 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: 0.820 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.014 0.075 10588 Z= 0.806 Angle : 1.587 11.290 14384 Z= 1.092 Chirality : 0.095 0.356 1572 Planarity : 0.013 0.222 1804 Dihedral : 10.600 75.590 3676 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 1.77 % Favored : 96.45 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1288 helix: None (None), residues: 0 sheet: 1.06 (0.24), residues: 444 loop : -0.43 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 220 TYR 0.033 0.005 TYR D 276 PHE 0.021 0.004 PHE D 406 TRP 0.025 0.005 TRP B 179 HIS 0.003 0.002 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.01353 / 0.81 (10548) covalent geometry : angle 1.54221 / 1.08 (14296) SS BOND : bond 0.01788 / 1.21 ( 32) SS BOND : angle 4.35737 / 2.72 ( 64) hydrogen bonds : bond 0.19215 / 13.61 ( 352) hydrogen bonds : angle 8.22711 / 5.81 ( 936) link_NAG-ASN : bond 0.02616 / 1.41 ( 8) link_NAG-ASN : angle 6.44533 / 3.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 0.272 Fit side-chains REVERT: A 119 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7160 (mmt90) REVERT: B 119 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7162 (mmt90) REVERT: C 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7155 (mmt90) REVERT: D 220 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7066 (mmt90) outliers start: 20 outliers final: 8 residues processed: 313 average time/residue: 0.1263 time to fit residues: 53.0269 Evaluate side-chains 185 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 185 HIS A 189 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS B 131 GLN B 185 HIS B 189 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS C 131 GLN C 185 HIS C 189 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 131 GLN D 185 HIS D 189 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.130206 restraints weight = 11131.638| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.15 r_work: 0.3233 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10588 Z= 0.135 Angle : 0.581 3.865 14384 Z= 0.328 Chirality : 0.048 0.146 1572 Planarity : 0.004 0.033 1804 Dihedral : 6.015 57.521 1420 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 2.13 % Allowed : 9.13 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1288 helix: -2.13 (0.34), residues: 24 sheet: 0.98 (0.21), residues: 496 loop : 0.10 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.008 0.001 TYR A 316 PHE 0.018 0.002 PHE D 406 TRP 0.015 0.001 TRP D 179 HIS 0.006 0.003 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (10548) covalent geometry : angle 0.57482 / 0.33 (14296) SS BOND : bond 0.00169 / 0.10 ( 32) SS BOND : angle 0.97408 / 0.61 ( 64) hydrogen bonds : bond 0.04980 / 3.38 ( 352) hydrogen bonds : angle 6.62086 / 4.65 ( 936) link_NAG-ASN : bond 0.00568 / 0.30 ( 8) link_NAG-ASN : angle 1.81391 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7146 (ttt180) cc_final: 0.6455 (mpt180) REVERT: A 390 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7639 (ttmm) REVERT: B 220 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6451 (mpt180) REVERT: B 390 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7642 (ttmm) REVERT: C 220 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6438 (mpt180) REVERT: D 220 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6456 (mpt180) REVERT: D 390 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7645 (ttmm) outliers start: 24 outliers final: 20 residues processed: 208 average time/residue: 0.0994 time to fit residues: 29.4631 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS B 185 HIS C 185 HIS D 185 HIS D 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121627 restraints weight = 11434.319| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.16 r_work: 0.3126 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10588 Z= 0.206 Angle : 0.581 4.140 14384 Z= 0.319 Chirality : 0.050 0.149 1572 Planarity : 0.005 0.039 1804 Dihedral : 4.890 17.451 1408 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.14 % Rotamer: Outliers : 2.93 % Allowed : 10.37 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1288 helix: -3.02 (0.24), residues: 24 sheet: 0.74 (0.21), residues: 556 loop : 0.10 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 156 TYR 0.007 0.001 TYR C 316 PHE 0.019 0.003 PHE B 406 TRP 0.017 0.002 TRP D 179 HIS 0.006 0.003 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (10548) covalent geometry : angle 0.57595 / 0.32 (14296) SS BOND : bond 0.00277 / 0.16 ( 32) SS BOND : angle 1.05915 / 0.65 ( 64) hydrogen bonds : bond 0.04543 / 3.06 ( 352) hydrogen bonds : angle 6.50653 / 4.59 ( 936) link_NAG-ASN : bond 0.00332 / 0.18 ( 8) link_NAG-ASN : angle 1.35467 / 0.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8639 (ptm160) cc_final: 0.8233 (ptm-80) REVERT: A 220 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6426 (mpt180) REVERT: A 380 TRP cc_start: 0.8427 (t-100) cc_final: 0.8134 (t-100) REVERT: B 118 ARG cc_start: 0.8638 (ptm160) cc_final: 0.8232 (ptm-80) REVERT: B 220 ARG cc_start: 0.7125 (ttt180) cc_final: 0.6427 (mpt180) REVERT: B 380 TRP cc_start: 0.8428 (t-100) cc_final: 0.8135 (t-100) REVERT: C 118 ARG cc_start: 0.8495 (ptm160) cc_final: 0.8211 (ptm-80) REVERT: C 220 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6420 (mpt180) REVERT: C 380 TRP cc_start: 0.8419 (t-100) cc_final: 0.8125 (t-100) REVERT: D 118 ARG cc_start: 0.8486 (ptm160) cc_final: 0.8207 (ptm-80) REVERT: D 220 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6434 (mpt180) REVERT: D 380 TRP cc_start: 0.8417 (t-100) cc_final: 0.8123 (t-100) outliers start: 33 outliers final: 28 residues processed: 197 average time/residue: 0.1367 time to fit residues: 35.4628 Evaluate side-chains 184 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.150723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120212 restraints weight = 11430.515| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.29 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10588 Z= 0.147 Angle : 0.511 3.818 14384 Z= 0.280 Chirality : 0.047 0.146 1572 Planarity : 0.005 0.040 1804 Dihedral : 4.692 17.702 1408 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.70 % Favored : 98.99 % Rotamer: Outliers : 2.84 % Allowed : 12.23 % Favored : 84.93 % 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: 0.28 (0.23), residues: 1288 helix: -3.11 (0.22), residues: 24 sheet: 0.60 (0.21), residues: 556 loop : 0.06 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 156 TYR 0.007 0.001 TYR B 316 PHE 0.016 0.002 PHE A 406 TRP 0.015 0.002 TRP C 179 HIS 0.005 0.002 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10548) covalent geometry : angle 0.50629 / 0.28 (14296) SS BOND : bond 0.00182 / 0.11 ( 32) SS BOND : angle 0.94635 / 0.58 ( 64) hydrogen bonds : bond 0.03885 / 2.61 ( 352) hydrogen bonds : angle 6.21887 / 4.38 ( 936) link_NAG-ASN : bond 0.00171 / 0.09 ( 8) link_NAG-ASN : angle 1.18172 / 0.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8245 (ptm-80) REVERT: A 220 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6290 (mpt180) REVERT: A 265 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7832 (tptp) REVERT: A 274 TYR cc_start: 0.7991 (m-80) cc_final: 0.7743 (m-80) REVERT: A 380 TRP cc_start: 0.8385 (t-100) cc_final: 0.8180 (t-100) REVERT: A 390 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7666 (ttmm) REVERT: B 118 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8268 (ptm-80) REVERT: B 220 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6291 (mpt180) REVERT: B 265 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7805 (tptp) REVERT: B 274 TYR cc_start: 0.7994 (m-80) cc_final: 0.7736 (m-80) REVERT: B 376 ASP cc_start: 0.7703 (t0) cc_final: 0.7376 (t0) REVERT: B 380 TRP cc_start: 0.8379 (t-100) cc_final: 0.8170 (t-100) REVERT: B 390 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7593 (ttmm) REVERT: C 118 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8354 (ptm-80) REVERT: C 220 ARG cc_start: 0.7005 (ttt180) cc_final: 0.6276 (mpt180) REVERT: C 265 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7828 (tptp) REVERT: C 274 TYR cc_start: 0.7980 (m-80) cc_final: 0.7716 (m-80) REVERT: C 380 TRP cc_start: 0.8373 (t-100) cc_final: 0.8170 (t-100) REVERT: D 118 ARG cc_start: 0.8656 (ptm160) cc_final: 0.8326 (ptm-80) REVERT: D 220 ARG cc_start: 0.7009 (ttt180) cc_final: 0.6305 (mpt180) REVERT: D 265 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7803 (tptp) REVERT: D 274 TYR cc_start: 0.7993 (m-80) cc_final: 0.7731 (m-80) REVERT: D 380 TRP cc_start: 0.8376 (t-100) cc_final: 0.8175 (t-100) REVERT: D 390 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7618 (ttmm) outliers start: 32 outliers final: 24 residues processed: 194 average time/residue: 0.1123 time to fit residues: 30.3634 Evaluate side-chains 190 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118187 restraints weight = 11486.070| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.29 r_work: 0.3076 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10588 Z= 0.173 Angle : 0.519 3.941 14384 Z= 0.283 Chirality : 0.048 0.150 1572 Planarity : 0.005 0.039 1804 Dihedral : 4.635 17.293 1408 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.94 % Favored : 97.75 % Rotamer: Outliers : 3.55 % Allowed : 11.79 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1288 helix: -3.27 (0.18), residues: 24 sheet: 0.44 (0.21), residues: 556 loop : -0.08 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 156 TYR 0.007 0.001 TYR B 316 PHE 0.018 0.003 PHE C 406 TRP 0.014 0.002 TRP D 179 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (10548) covalent geometry : angle 0.51409 / 0.28 (14296) SS BOND : bond 0.00189 / 0.11 ( 32) SS BOND : angle 0.94899 / 0.58 ( 64) hydrogen bonds : bond 0.04012 / 2.70 ( 352) hydrogen bonds : angle 6.18814 / 4.36 ( 936) link_NAG-ASN : bond 0.00160 / 0.09 ( 8) link_NAG-ASN : angle 1.31259 / 0.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.309 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: A 118 ARG cc_start: 0.8709 (ptm160) cc_final: 0.8351 (ptm-80) REVERT: A 220 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6272 (mpt180) REVERT: A 265 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7685 (tptp) REVERT: A 376 ASP cc_start: 0.7828 (t0) cc_final: 0.7478 (t0) REVERT: A 380 TRP cc_start: 0.8350 (t-100) cc_final: 0.8146 (t-100) REVERT: B 118 ARG cc_start: 0.8712 (ptm160) cc_final: 0.8351 (ptm-80) REVERT: B 220 ARG cc_start: 0.7001 (ttt180) cc_final: 0.6271 (mpt180) REVERT: B 265 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (tptp) REVERT: B 376 ASP cc_start: 0.7840 (t0) cc_final: 0.7498 (t0) REVERT: C 118 ARG cc_start: 0.8623 (ptm160) cc_final: 0.8297 (ptm-80) REVERT: C 220 ARG cc_start: 0.7004 (ttt180) cc_final: 0.6270 (mpt180) REVERT: C 265 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7681 (tptp) REVERT: C 376 ASP cc_start: 0.7836 (t0) cc_final: 0.7495 (t0) REVERT: D 118 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8329 (ptm-80) REVERT: D 220 ARG cc_start: 0.6984 (ttt180) cc_final: 0.6278 (mpt180) REVERT: D 265 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7686 (tptp) REVERT: D 376 ASP cc_start: 0.7829 (t0) cc_final: 0.7480 (t0) outliers start: 40 outliers final: 24 residues processed: 185 average time/residue: 0.1141 time to fit residues: 29.3088 Evaluate side-chains 183 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120278 restraints weight = 11441.310| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.42 r_work: 0.3111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10588 Z= 0.095 Angle : 0.458 3.695 14384 Z= 0.252 Chirality : 0.046 0.144 1572 Planarity : 0.004 0.040 1804 Dihedral : 4.389 17.242 1408 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.39 % Favored : 99.30 % Rotamer: Outliers : 2.13 % Allowed : 13.21 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1288 helix: -2.88 (0.24), residues: 24 sheet: 0.58 (0.22), residues: 528 loop : -0.06 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.007 0.001 TYR B 316 PHE 0.012 0.002 PHE A 121 TRP 0.011 0.001 TRP C 179 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10548) covalent geometry : angle 0.45445 / 0.25 (14296) SS BOND : bond 0.00149 / 0.09 ( 32) SS BOND : angle 0.77954 / 0.47 ( 64) hydrogen bonds : bond 0.03292 / 2.22 ( 352) hydrogen bonds : angle 5.96680 / 4.20 ( 936) link_NAG-ASN : bond 0.00104 / 0.06 ( 8) link_NAG-ASN : angle 1.07800 / 0.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8392 (ptm-80) REVERT: A 198 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: A 220 ARG cc_start: 0.6926 (ttt180) cc_final: 0.6183 (mpt180) REVERT: A 376 ASP cc_start: 0.7804 (t0) cc_final: 0.7479 (t0) REVERT: B 118 ARG cc_start: 0.8728 (ptm160) cc_final: 0.8378 (ptm-80) REVERT: B 198 PRO cc_start: 0.7679 (Cg_exo) cc_final: 0.7431 (Cg_endo) REVERT: B 220 ARG cc_start: 0.6925 (ttt180) cc_final: 0.6176 (mpt180) REVERT: B 376 ASP cc_start: 0.7815 (t0) cc_final: 0.7493 (t0) REVERT: C 118 ARG cc_start: 0.8659 (ptm160) cc_final: 0.8360 (ptm-80) REVERT: C 198 PRO cc_start: 0.7675 (Cg_exo) cc_final: 0.7432 (Cg_endo) REVERT: C 220 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6178 (mpt180) REVERT: C 376 ASP cc_start: 0.7802 (t0) cc_final: 0.7477 (t0) REVERT: D 118 ARG cc_start: 0.8657 (ptm160) cc_final: 0.8356 (ptm-80) REVERT: D 198 PRO cc_start: 0.7671 (Cg_exo) cc_final: 0.7431 (Cg_endo) REVERT: D 220 ARG cc_start: 0.6948 (ttt180) cc_final: 0.6202 (mpt180) REVERT: D 376 ASP cc_start: 0.7800 (t0) cc_final: 0.7473 (t0) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.1161 time to fit residues: 28.2600 Evaluate side-chains 171 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120623 restraints weight = 11363.983| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.31 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10588 Z= 0.104 Angle : 0.467 3.829 14384 Z= 0.255 Chirality : 0.047 0.145 1572 Planarity : 0.004 0.039 1804 Dihedral : 4.341 17.003 1408 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.01 % Favored : 98.68 % Rotamer: Outliers : 2.04 % Allowed : 14.54 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1288 helix: -2.94 (0.22), residues: 24 sheet: 0.50 (0.22), residues: 528 loop : 0.02 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 156 TYR 0.009 0.001 TYR D 316 PHE 0.014 0.002 PHE D 121 TRP 0.010 0.001 TRP B 179 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (10548) covalent geometry : angle 0.46321 / 0.25 (14296) SS BOND : bond 0.00134 / 0.09 ( 32) SS BOND : angle 0.78973 / 0.48 ( 64) hydrogen bonds : bond 0.03297 / 2.22 ( 352) hydrogen bonds : angle 5.93577 / 4.17 ( 936) link_NAG-ASN : bond 0.00135 / 0.07 ( 8) link_NAG-ASN : angle 1.07099 / 0.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8701 (ptm160) cc_final: 0.8389 (ptm-80) REVERT: A 198 PRO cc_start: 0.7706 (Cg_exo) cc_final: 0.7466 (Cg_endo) REVERT: A 220 ARG cc_start: 0.6941 (ttt180) cc_final: 0.6219 (mpt180) REVERT: A 376 ASP cc_start: 0.7818 (t0) cc_final: 0.7497 (t0) REVERT: B 118 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8370 (ptm-80) REVERT: B 198 PRO cc_start: 0.7707 (Cg_exo) cc_final: 0.7465 (Cg_endo) REVERT: B 220 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6212 (mpt180) REVERT: B 376 ASP cc_start: 0.7840 (t0) cc_final: 0.7516 (t0) REVERT: C 118 ARG cc_start: 0.8664 (ptm160) cc_final: 0.8376 (ptm-80) REVERT: C 128 GLU cc_start: 0.8147 (pt0) cc_final: 0.7759 (pt0) REVERT: C 198 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7452 (Cg_endo) REVERT: C 220 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6193 (mpt180) REVERT: C 376 ASP cc_start: 0.7828 (t0) cc_final: 0.7508 (t0) REVERT: D 118 ARG cc_start: 0.8624 (ptm160) cc_final: 0.8339 (ptm-80) REVERT: D 128 GLU cc_start: 0.8151 (pt0) cc_final: 0.7761 (pt0) REVERT: D 198 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7455 (Cg_endo) REVERT: D 220 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6236 (mpt180) REVERT: D 376 ASP cc_start: 0.7832 (t0) cc_final: 0.7499 (t0) outliers start: 23 outliers final: 20 residues processed: 164 average time/residue: 0.1104 time to fit residues: 25.0607 Evaluate side-chains 170 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120834 restraints weight = 11418.609| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.32 r_work: 0.3113 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10588 Z= 0.100 Angle : 0.458 3.720 14384 Z= 0.251 Chirality : 0.046 0.143 1572 Planarity : 0.004 0.039 1804 Dihedral : 4.296 16.893 1408 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.79 % Favored : 97.90 % Rotamer: Outliers : 2.39 % Allowed : 13.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.23), residues: 1288 helix: -2.90 (0.23), residues: 24 sheet: 0.59 (0.22), residues: 536 loop : 0.11 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 156 TYR 0.007 0.001 TYR D 316 PHE 0.013 0.002 PHE C 121 TRP 0.010 0.001 TRP A 179 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (10548) covalent geometry : angle 0.45415 / 0.25 (14296) SS BOND : bond 0.00130 / 0.08 ( 32) SS BOND : angle 0.77640 / 0.47 ( 64) hydrogen bonds : bond 0.03242 / 2.18 ( 352) hydrogen bonds : angle 5.86781 / 4.12 ( 936) link_NAG-ASN : bond 0.00132 / 0.07 ( 8) link_NAG-ASN : angle 1.05136 / 0.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8724 (ptm160) cc_final: 0.8423 (ptm-80) REVERT: A 198 PRO cc_start: 0.7784 (Cg_exo) cc_final: 0.7566 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6179 (mpt180) REVERT: A 376 ASP cc_start: 0.7855 (t0) cc_final: 0.7510 (t0) REVERT: B 118 ARG cc_start: 0.8715 (ptm160) cc_final: 0.8427 (ptm-80) REVERT: B 198 PRO cc_start: 0.7725 (Cg_exo) cc_final: 0.7504 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6174 (mpt180) REVERT: B 376 ASP cc_start: 0.7853 (t0) cc_final: 0.7531 (t0) REVERT: C 118 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8419 (ptm-80) REVERT: C 136 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8705 (tp40) REVERT: C 198 PRO cc_start: 0.7716 (Cg_exo) cc_final: 0.7493 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6155 (mpt180) REVERT: C 376 ASP cc_start: 0.7867 (t0) cc_final: 0.7539 (t0) REVERT: D 118 ARG cc_start: 0.8644 (ptm160) cc_final: 0.8369 (ptm-80) REVERT: D 198 PRO cc_start: 0.7716 (Cg_exo) cc_final: 0.7498 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6187 (mpt180) REVERT: D 376 ASP cc_start: 0.7850 (t0) cc_final: 0.7520 (t0) outliers start: 27 outliers final: 24 residues processed: 170 average time/residue: 0.1015 time to fit residues: 24.4844 Evaluate side-chains 180 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.150929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119171 restraints weight = 11414.670| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.41 r_work: 0.3101 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10588 Z= 0.125 Angle : 0.483 3.803 14384 Z= 0.262 Chirality : 0.047 0.153 1572 Planarity : 0.004 0.038 1804 Dihedral : 4.324 16.715 1408 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.48 % Favored : 98.21 % Rotamer: Outliers : 2.75 % Allowed : 13.56 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1288 helix: -3.00 (0.21), residues: 24 sheet: 0.47 (0.22), residues: 564 loop : 0.18 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 156 TYR 0.011 0.001 TYR D 274 PHE 0.015 0.002 PHE C 121 TRP 0.009 0.001 TRP B 179 HIS 0.004 0.002 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10548) covalent geometry : angle 0.47926 / 0.26 (14296) SS BOND : bond 0.00138 / 0.08 ( 32) SS BOND : angle 0.81805 / 0.50 ( 64) hydrogen bonds : bond 0.03403 / 2.29 ( 352) hydrogen bonds : angle 5.88635 / 4.13 ( 936) link_NAG-ASN : bond 0.00132 / 0.07 ( 8) link_NAG-ASN : angle 1.10011 / 0.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8749 (ptm160) cc_final: 0.8455 (ptm-80) REVERT: A 198 PRO cc_start: 0.7806 (Cg_exo) cc_final: 0.7557 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6142 (mpt180) REVERT: A 376 ASP cc_start: 0.8092 (t0) cc_final: 0.7778 (t0) REVERT: B 118 ARG cc_start: 0.8745 (ptm160) cc_final: 0.8446 (ptm-80) REVERT: B 198 PRO cc_start: 0.7805 (Cg_exo) cc_final: 0.7556 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6144 (mpt180) REVERT: B 277 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: B 376 ASP cc_start: 0.8071 (t0) cc_final: 0.7779 (t0) REVERT: C 118 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8404 (ptm-80) REVERT: C 198 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6133 (mpt180) REVERT: C 376 ASP cc_start: 0.8117 (t0) cc_final: 0.7811 (t0) REVERT: D 118 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8370 (ptm-80) REVERT: D 198 PRO cc_start: 0.7709 (Cg_exo) cc_final: 0.7487 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7178 (ttt180) cc_final: 0.6156 (mpt180) REVERT: D 376 ASP cc_start: 0.8077 (t0) cc_final: 0.7779 (t0) outliers start: 31 outliers final: 28 residues processed: 170 average time/residue: 0.0929 time to fit residues: 22.3997 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 273 ASN D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.118076 restraints weight = 11362.659| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.30 r_work: 0.3087 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10588 Z= 0.167 Angle : 0.516 3.965 14384 Z= 0.279 Chirality : 0.048 0.166 1572 Planarity : 0.005 0.037 1804 Dihedral : 4.442 16.643 1408 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.87 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 14.01 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1288 helix: -3.14 (0.19), residues: 24 sheet: 0.34 (0.21), residues: 564 loop : 0.13 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 156 TYR 0.009 0.001 TYR B 274 PHE 0.017 0.002 PHE D 121 TRP 0.009 0.002 TRP C 179 HIS 0.005 0.002 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (10548) covalent geometry : angle 0.51142 / 0.28 (14296) SS BOND : bond 0.00140 / 0.08 ( 32) SS BOND : angle 0.89957 / 0.55 ( 64) hydrogen bonds : bond 0.03729 / 2.49 ( 352) hydrogen bonds : angle 6.03222 / 4.24 ( 936) link_NAG-ASN : bond 0.00114 / 0.06 ( 8) link_NAG-ASN : angle 1.26889 / 0.75 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8687 (ptm160) cc_final: 0.8387 (ptm-80) REVERT: A 198 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6151 (mpt180) REVERT: A 277 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 376 ASP cc_start: 0.8173 (t0) cc_final: 0.7840 (t0) REVERT: B 118 ARG cc_start: 0.8733 (ptm160) cc_final: 0.8417 (ptm-80) REVERT: B 198 PRO cc_start: 0.7827 (Cg_exo) cc_final: 0.7590 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6147 (mpt180) REVERT: B 376 ASP cc_start: 0.8178 (t0) cc_final: 0.7860 (t0) REVERT: C 118 ARG cc_start: 0.8637 (ptm160) cc_final: 0.8352 (ptm-80) REVERT: C 152 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7157 (mtm-85) REVERT: C 198 PRO cc_start: 0.7817 (Cg_exo) cc_final: 0.7583 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6153 (mpt180) REVERT: C 277 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: C 376 ASP cc_start: 0.8197 (t0) cc_final: 0.7872 (t0) REVERT: D 118 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8336 (ptm-80) REVERT: D 198 PRO cc_start: 0.7799 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7119 (ttt180) cc_final: 0.6159 (mpt180) REVERT: D 277 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: D 312 TYR cc_start: 0.8971 (p90) cc_final: 0.8671 (p90) REVERT: D 376 ASP cc_start: 0.8178 (t0) cc_final: 0.7856 (t0) outliers start: 34 outliers final: 27 residues processed: 181 average time/residue: 0.1045 time to fit residues: 25.7310 Evaluate side-chains 180 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 0.0470 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 136 GLN C 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119674 restraints weight = 11397.478| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.43 r_work: 0.3096 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10588 Z= 0.112 Angle : 0.481 3.797 14384 Z= 0.263 Chirality : 0.047 0.163 1572 Planarity : 0.004 0.038 1804 Dihedral : 4.395 16.591 1408 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.14 % Rotamer: Outliers : 2.75 % Allowed : 14.72 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1288 helix: -2.88 (0.24), residues: 24 sheet: 0.51 (0.22), residues: 536 loop : 0.01 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 156 TYR 0.008 0.001 TYR D 316 PHE 0.014 0.002 PHE C 121 TRP 0.011 0.001 TRP B 179 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (10548) covalent geometry : angle 0.47678 / 0.26 (14296) SS BOND : bond 0.00124 / 0.08 ( 32) SS BOND : angle 0.78497 / 0.48 ( 64) hydrogen bonds : bond 0.03357 / 2.26 ( 352) hydrogen bonds : angle 5.94157 / 4.16 ( 936) link_NAG-ASN : bond 0.00091 / 0.05 ( 8) link_NAG-ASN : angle 1.18654 / 0.71 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.61 seconds wall clock time: 44 minutes 48.76 seconds (2688.76 seconds total)