Starting phenix.real_space_refine on Wed Mar 4 02:57:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2t_26319/03_2026/7u2t_26319.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2t_26319/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u2t_26319/03_2026/7u2t_26319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2t_26319/03_2026/7u2t_26319.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2t_26319/03_2026/7u2t_26319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2t_26319/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 1.43, per 1000 atoms: 0.14 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: 0.67 Conformation dependent library (CDL) restraints added in 499.3 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: 0.24 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: 1.37 Time building geometry restraints manager: 0.97 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: 6008 15.12 - 30.24: 236 30.24 - 45.35: 60 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 6348 sinusoidal: 2584 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 6345 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: 0.03 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.160 Find NCS groups from input model: 0.080 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 10.503 75.590 3844 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 covalent geometry : bond 0.01353 (10548) covalent geometry : angle 1.54221 (14296) SS BOND : bond 0.01788 ( 32) SS BOND : angle 4.35737 ( 64) hydrogen bonds : bond 0.19215 ( 352) hydrogen bonds : angle 8.22711 ( 936) link_NAG-ASN : bond 0.02616 ( 8) link_NAG-ASN : angle 6.44533 ( 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 : 0.386 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: 0.1179 time to fit residues: 49.3088 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 : 0.375 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 185 HIS A 189 ASN A 409 HIS B 131 GLN B 185 HIS B 189 ASN B 409 HIS C 131 GLN C 185 HIS C 189 ASN C 409 HIS D 131 GLN D 185 HIS D 189 ASN D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130354 restraints weight = 11118.881| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.16 r_work: 0.3236 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2390 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= 0.124 Angle : 0.567 3.864 14384 Z= 0.319 Chirality : 0.048 0.150 1572 Planarity : 0.004 0.034 1804 Dihedral : 7.195 59.607 1588 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 2.13 % Allowed : 9.04 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1288 helix: -2.33 (0.32), residues: 24 sheet: 0.98 (0.21), residues: 496 loop : 0.07 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.010 0.001 TYR A 316 PHE 0.018 0.002 PHE D 406 TRP 0.015 0.001 TRP A 179 HIS 0.007 0.003 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00273 (10548) covalent geometry : angle 0.56199 (14296) SS BOND : bond 0.00199 ( 32) SS BOND : angle 0.89899 ( 64) hydrogen bonds : bond 0.04751 ( 352) hydrogen bonds : angle 6.62548 ( 936) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 1.60406 ( 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 213 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7060 (ttt180) cc_final: 0.6327 (mpt180) REVERT: A 390 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7626 (ttmm) REVERT: B 220 ARG cc_start: 0.7058 (ttt180) cc_final: 0.6323 (mpt180) REVERT: B 390 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7632 (ttmm) REVERT: C 220 ARG cc_start: 0.7057 (ttt180) cc_final: 0.6314 (mpt180) REVERT: C 390 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7635 (ttmm) REVERT: D 220 ARG cc_start: 0.7074 (ttt180) cc_final: 0.6335 (mpt180) REVERT: D 390 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7634 (ttmm) outliers start: 24 outliers final: 20 residues processed: 209 average time/residue: 0.0943 time to fit residues: 27.8793 Evaluate side-chains 183 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 185 HIS B 300 ASN C 185 HIS D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122058 restraints weight = 11452.738| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.15 r_work: 0.3134 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10588 Z= 0.202 Angle : 0.574 3.991 14384 Z= 0.316 Chirality : 0.050 0.151 1572 Planarity : 0.005 0.039 1804 Dihedral : 6.164 57.348 1576 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.14 % Rotamer: Outliers : 2.93 % Allowed : 10.20 % Favored : 86.88 % 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: 0.44 (0.23), residues: 1288 helix: -3.07 (0.24), residues: 24 sheet: 0.77 (0.21), residues: 556 loop : 0.12 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 156 TYR 0.006 0.001 TYR C 316 PHE 0.018 0.003 PHE B 406 TRP 0.018 0.002 TRP A 179 HIS 0.005 0.003 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00488 (10548) covalent geometry : angle 0.56910 (14296) SS BOND : bond 0.00210 ( 32) SS BOND : angle 1.03583 ( 64) hydrogen bonds : bond 0.04521 ( 352) hydrogen bonds : angle 6.52238 ( 936) link_NAG-ASN : bond 0.00282 ( 8) link_NAG-ASN : angle 1.33625 ( 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 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.378 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: 0.8226 (ptm-80) REVERT: A 220 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6446 (mpt180) REVERT: B 118 ARG cc_start: 0.8637 (ptm160) cc_final: 0.8223 (ptm-80) REVERT: B 220 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6450 (mpt180) REVERT: C 220 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6442 (mpt180) REVERT: D 220 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6447 (mpt180) outliers start: 33 outliers final: 28 residues processed: 200 average time/residue: 0.1277 time to fit residues: 33.5676 Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.148957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118410 restraints weight = 11433.595| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.29 r_work: 0.3082 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10588 Z= 0.186 Angle : 0.542 3.978 14384 Z= 0.296 Chirality : 0.049 0.150 1572 Planarity : 0.005 0.040 1804 Dihedral : 6.044 55.963 1576 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.32 % Favored : 98.37 % Rotamer: Outliers : 3.19 % Allowed : 11.61 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1288 helix: -3.41 (0.19), residues: 24 sheet: 0.59 (0.22), residues: 548 loop : -0.14 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 156 TYR 0.006 0.001 TYR D 353 PHE 0.019 0.002 PHE B 406 TRP 0.015 0.002 TRP B 179 HIS 0.005 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00454 (10548) covalent geometry : angle 0.53653 (14296) SS BOND : bond 0.00205 ( 32) SS BOND : angle 1.05117 ( 64) hydrogen bonds : bond 0.04102 ( 352) hydrogen bonds : angle 6.28775 ( 936) link_NAG-ASN : bond 0.00200 ( 8) link_NAG-ASN : angle 1.25615 ( 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 199 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 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: 0.8625 (ptm160) cc_final: 0.8275 (ptm-80) REVERT: A 220 ARG cc_start: 0.6997 (ttt180) cc_final: 0.6244 (mpt180) REVERT: A 265 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7772 (tptp) REVERT: A 376 ASP cc_start: 0.7986 (t0) cc_final: 0.7663 (t0) REVERT: A 380 TRP cc_start: 0.8411 (t-100) cc_final: 0.8193 (t-100) REVERT: A 390 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7653 (ttmm) REVERT: B 118 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8280 (ptm-80) REVERT: B 220 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6248 (mpt180) REVERT: B 265 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7768 (tptp) REVERT: B 274 TYR cc_start: 0.8021 (m-80) cc_final: 0.7768 (m-80) REVERT: B 376 ASP cc_start: 0.8004 (t0) cc_final: 0.7691 (t0) REVERT: B 380 TRP cc_start: 0.8403 (t-100) cc_final: 0.8178 (t-100) REVERT: B 390 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7661 (ttmm) REVERT: C 118 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8326 (ptm-80) REVERT: C 220 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6253 (mpt180) REVERT: C 265 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7766 (tptp) REVERT: C 278 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 376 ASP cc_start: 0.7993 (t0) cc_final: 0.7680 (t0) REVERT: C 380 TRP cc_start: 0.8400 (t-100) cc_final: 0.8182 (t-100) REVERT: C 390 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7674 (ttmm) REVERT: D 118 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8327 (ptm-80) REVERT: D 220 ARG cc_start: 0.7005 (ttt180) cc_final: 0.6270 (mpt180) REVERT: D 265 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (tptp) REVERT: D 376 ASP cc_start: 0.7985 (t0) cc_final: 0.7664 (t0) REVERT: D 380 TRP cc_start: 0.8399 (t-100) cc_final: 0.8184 (t-100) REVERT: D 390 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7672 (ttmm) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.1082 time to fit residues: 27.6122 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 : 0.379 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117930 restraints weight = 11425.741| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.40 r_work: 0.3091 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10588 Z= 0.150 Angle : 0.501 3.902 14384 Z= 0.275 Chirality : 0.047 0.148 1572 Planarity : 0.005 0.039 1804 Dihedral : 5.907 55.584 1576 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.48 % Favored : 98.21 % Rotamer: Outliers : 3.19 % Allowed : 11.61 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.23), residues: 1288 helix: -3.30 (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 0.004 0.000 ARG A 156 TYR 0.007 0.001 TYR C 316 PHE 0.017 0.002 PHE D 121 TRP 0.014 0.001 TRP D 179 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00367 (10548) covalent geometry : angle 0.49660 (14296) SS BOND : bond 0.00163 ( 32) SS BOND : angle 0.87791 ( 64) hydrogen bonds : bond 0.03790 ( 352) hydrogen bonds : angle 6.16188 ( 936) link_NAG-ASN : bond 0.00136 ( 8) link_NAG-ASN : angle 1.20694 ( 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 206 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8707 (ptm160) cc_final: 0.8340 (ptm-80) REVERT: A 220 ARG cc_start: 0.6998 (ttt180) cc_final: 0.6266 (mpt180) REVERT: A 265 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7644 (tptp) REVERT: A 376 ASP cc_start: 0.7827 (t0) cc_final: 0.7468 (t0) REVERT: A 380 TRP cc_start: 0.8346 (t-100) cc_final: 0.8126 (t-100) REVERT: B 118 ARG cc_start: 0.8717 (ptm160) cc_final: 0.8347 (ptm-80) REVERT: B 220 ARG cc_start: 0.6892 (ttt180) cc_final: 0.6103 (mpt180) REVERT: B 376 ASP cc_start: 0.7854 (t0) cc_final: 0.7501 (t0) REVERT: B 380 TRP cc_start: 0.8337 (t-100) cc_final: 0.8121 (t-100) REVERT: C 118 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8286 (ptm-80) REVERT: C 128 GLU cc_start: 0.8119 (pt0) cc_final: 0.7816 (pt0) REVERT: C 220 ARG cc_start: 0.6896 (ttt180) cc_final: 0.6101 (mpt180) REVERT: C 265 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7643 (tptp) REVERT: C 376 ASP cc_start: 0.7856 (t0) cc_final: 0.7502 (t0) REVERT: C 380 TRP cc_start: 0.8330 (t-100) cc_final: 0.8113 (t-100) REVERT: D 118 ARG cc_start: 0.8658 (ptm160) cc_final: 0.8318 (ptm-80) REVERT: D 220 ARG cc_start: 0.7000 (ttt180) cc_final: 0.6265 (mpt180) REVERT: D 376 ASP cc_start: 0.7830 (t0) cc_final: 0.7468 (t0) REVERT: D 380 TRP cc_start: 0.8330 (t-100) cc_final: 0.8120 (t-100) outliers start: 36 outliers final: 24 residues processed: 186 average time/residue: 0.1017 time to fit residues: 25.9847 Evaluate side-chains 182 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118859 restraints weight = 11471.983| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.32 r_work: 0.3086 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10588 Z= 0.140 Angle : 0.492 3.871 14384 Z= 0.269 Chirality : 0.047 0.146 1572 Planarity : 0.005 0.039 1804 Dihedral : 5.810 55.432 1576 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.63 % Favored : 98.06 % Rotamer: Outliers : 2.66 % Allowed : 13.39 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1288 helix: -3.10 (0.22), residues: 24 sheet: 0.36 (0.21), residues: 556 loop : 0.02 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 156 TYR 0.007 0.001 TYR B 316 PHE 0.015 0.002 PHE D 121 TRP 0.013 0.001 TRP B 179 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00342 (10548) covalent geometry : angle 0.48782 (14296) SS BOND : bond 0.00171 ( 32) SS BOND : angle 0.87445 ( 64) hydrogen bonds : bond 0.03652 ( 352) hydrogen bonds : angle 6.04771 ( 936) link_NAG-ASN : bond 0.00162 ( 8) link_NAG-ASN : angle 1.15880 ( 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 192 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8719 (ptm160) cc_final: 0.8345 (ptm-80) REVERT: A 198 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7511 (Cg_endo) REVERT: A 220 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6171 (mpt180) REVERT: A 376 ASP cc_start: 0.7851 (t0) cc_final: 0.7502 (t0) REVERT: A 380 TRP cc_start: 0.8389 (t-100) cc_final: 0.8179 (t-100) REVERT: B 118 ARG cc_start: 0.8728 (ptm160) cc_final: 0.8352 (ptm-80) REVERT: B 128 GLU cc_start: 0.8113 (pt0) cc_final: 0.7760 (pt0) REVERT: B 198 PRO cc_start: 0.7772 (Cg_exo) cc_final: 0.7507 (Cg_endo) REVERT: B 220 ARG cc_start: 0.6928 (ttt180) cc_final: 0.6155 (mpt180) REVERT: B 376 ASP cc_start: 0.7876 (t0) cc_final: 0.7547 (t0) REVERT: B 380 TRP cc_start: 0.8385 (t-100) cc_final: 0.8173 (t-100) REVERT: C 118 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8294 (ptm-80) REVERT: C 128 GLU cc_start: 0.8108 (pt0) cc_final: 0.7758 (pt0) REVERT: C 198 PRO cc_start: 0.7759 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: C 220 ARG cc_start: 0.6930 (ttt180) cc_final: 0.6167 (mpt180) REVERT: C 227 GLN cc_start: 0.9010 (mt0) cc_final: 0.8782 (mt0) REVERT: C 376 ASP cc_start: 0.7872 (t0) cc_final: 0.7538 (t0) REVERT: C 380 TRP cc_start: 0.8371 (t-100) cc_final: 0.8167 (t-100) REVERT: D 118 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8339 (ptm-80) REVERT: D 128 GLU cc_start: 0.8097 (pt0) cc_final: 0.7744 (pt0) REVERT: D 198 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.7509 (Cg_endo) REVERT: D 220 ARG cc_start: 0.6991 (ttt180) cc_final: 0.6232 (mpt180) REVERT: D 376 ASP cc_start: 0.7858 (t0) cc_final: 0.7520 (t0) outliers start: 30 outliers final: 24 residues processed: 176 average time/residue: 0.1168 time to fit residues: 27.9391 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 227 GLN C 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.148699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117637 restraints weight = 11335.059| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.32 r_work: 0.3087 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10588 Z= 0.159 Angle : 0.504 3.915 14384 Z= 0.274 Chirality : 0.048 0.149 1572 Planarity : 0.005 0.038 1804 Dihedral : 5.852 56.050 1576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.86 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 13.03 % Favored : 84.22 % 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: 0.10 (0.23), residues: 1288 helix: -3.00 (0.25), residues: 24 sheet: 0.33 (0.21), residues: 564 loop : 0.08 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 156 TYR 0.006 0.001 TYR C 316 PHE 0.016 0.002 PHE C 121 TRP 0.012 0.002 TRP C 179 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00392 (10548) covalent geometry : angle 0.49966 (14296) SS BOND : bond 0.00160 ( 32) SS BOND : angle 0.89978 ( 64) hydrogen bonds : bond 0.03729 ( 352) hydrogen bonds : angle 6.07953 ( 936) link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 1.22998 ( 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 201 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8727 (ptm160) cc_final: 0.8365 (ptm-80) REVERT: A 198 PRO cc_start: 0.7800 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6150 (mpt180) REVERT: A 376 ASP cc_start: 0.7923 (t0) cc_final: 0.7576 (t0) REVERT: A 380 TRP cc_start: 0.8394 (t-100) cc_final: 0.8159 (t-100) REVERT: B 118 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8357 (ptm-80) REVERT: B 152 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7162 (mtm-85) REVERT: B 198 PRO cc_start: 0.7808 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6132 (mpt180) REVERT: B 273 ASN cc_start: 0.7700 (m-40) cc_final: 0.7488 (p0) REVERT: B 376 ASP cc_start: 0.7954 (t0) cc_final: 0.7607 (t0) REVERT: C 118 ARG cc_start: 0.8653 (ptm160) cc_final: 0.8326 (ptm-80) REVERT: C 128 GLU cc_start: 0.8116 (pt0) cc_final: 0.7743 (pt0) REVERT: C 152 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7144 (mtm-85) REVERT: C 198 PRO cc_start: 0.7792 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6154 (mpt180) REVERT: C 376 ASP cc_start: 0.7950 (t0) cc_final: 0.7607 (t0) REVERT: D 118 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8324 (ptm-80) REVERT: D 152 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: D 198 PRO cc_start: 0.7783 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6167 (mpt180) REVERT: D 273 ASN cc_start: 0.7686 (m-40) cc_final: 0.7479 (p0) REVERT: D 376 ASP cc_start: 0.7934 (t0) cc_final: 0.7574 (t0) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 0.1227 time to fit residues: 30.6241 Evaluate side-chains 186 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN C 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118622 restraints weight = 11347.097| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.32 r_work: 0.3094 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10588 Z= 0.127 Angle : 0.487 3.929 14384 Z= 0.266 Chirality : 0.047 0.153 1572 Planarity : 0.004 0.038 1804 Dihedral : 5.784 55.642 1576 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.79 % Favored : 97.90 % Rotamer: Outliers : 2.93 % Allowed : 13.65 % 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: 0.12 (0.23), residues: 1288 helix: -2.92 (0.25), residues: 24 sheet: 0.32 (0.21), residues: 564 loop : 0.12 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 156 TYR 0.007 0.001 TYR B 316 PHE 0.015 0.002 PHE C 121 TRP 0.012 0.001 TRP B 179 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00307 (10548) covalent geometry : angle 0.48282 (14296) SS BOND : bond 0.00142 ( 32) SS BOND : angle 0.83564 ( 64) hydrogen bonds : bond 0.03524 ( 352) hydrogen bonds : angle 6.00029 ( 936) link_NAG-ASN : bond 0.00133 ( 8) link_NAG-ASN : angle 1.16800 ( 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 206 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8701 (ptm160) cc_final: 0.8368 (ptm-80) REVERT: A 152 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7125 (mtm-85) REVERT: A 198 PRO cc_start: 0.7796 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6144 (mpt180) REVERT: A 376 ASP cc_start: 0.7940 (t0) cc_final: 0.7594 (t0) REVERT: B 118 ARG cc_start: 0.8714 (ptm160) cc_final: 0.8366 (ptm-80) REVERT: B 128 GLU cc_start: 0.8103 (pt0) cc_final: 0.7709 (pt0) REVERT: B 152 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: B 198 PRO cc_start: 0.7802 (Cg_exo) cc_final: 0.7580 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7134 (ttt180) cc_final: 0.6129 (mpt180) REVERT: B 376 ASP cc_start: 0.7949 (t0) cc_final: 0.7609 (t0) REVERT: C 118 ARG cc_start: 0.8656 (ptm160) cc_final: 0.8335 (ptm-80) REVERT: C 152 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.7087 (mtm-85) REVERT: C 198 PRO cc_start: 0.7807 (Cg_exo) cc_final: 0.7584 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7134 (ttt180) cc_final: 0.6129 (mpt180) REVERT: C 277 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: C 376 ASP cc_start: 0.7945 (t0) cc_final: 0.7607 (t0) REVERT: D 118 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8335 (ptm-80) REVERT: D 152 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7100 (mtm-85) REVERT: D 198 PRO cc_start: 0.7803 (Cg_exo) cc_final: 0.7579 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6165 (mpt180) REVERT: D 273 ASN cc_start: 0.7688 (m-40) cc_final: 0.7473 (p0) REVERT: D 376 ASP cc_start: 0.8119 (t0) cc_final: 0.7783 (t0) outliers start: 33 outliers final: 29 residues processed: 192 average time/residue: 0.1261 time to fit residues: 32.2956 Evaluate side-chains 199 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 127 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 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 = 0.3574 r_free = 0.3574 target = 0.146670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.115193 restraints weight = 11392.917| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.33 r_work: 0.3034 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10588 Z= 0.227 Angle : 0.565 4.284 14384 Z= 0.305 Chirality : 0.050 0.155 1572 Planarity : 0.005 0.036 1804 Dihedral : 6.108 57.951 1576 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.34 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 14.27 % Favored : 82.71 % 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: -0.19 (0.23), residues: 1288 helix: -3.37 (0.19), residues: 24 sheet: 0.12 (0.21), residues: 564 loop : -0.10 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 156 TYR 0.010 0.001 TYR B 274 PHE 0.022 0.003 PHE C 406 TRP 0.012 0.002 TRP A 179 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00561 (10548) covalent geometry : angle 0.55967 (14296) SS BOND : bond 0.00198 ( 32) SS BOND : angle 1.03509 ( 64) hydrogen bonds : bond 0.04213 ( 352) hydrogen bonds : angle 6.26639 ( 936) link_NAG-ASN : bond 0.00188 ( 8) link_NAG-ASN : angle 1.42998 ( 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 201 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8323 (ptm-80) REVERT: A 152 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: A 220 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6018 (mpt180) REVERT: A 376 ASP cc_start: 0.8244 (t0) cc_final: 0.7886 (t0) REVERT: A 380 TRP cc_start: 0.8320 (t-100) cc_final: 0.8092 (t-100) REVERT: B 118 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8319 (ptm-80) REVERT: B 152 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: B 198 PRO cc_start: 0.7809 (Cg_exo) cc_final: 0.7589 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7267 (ttt180) cc_final: 0.6148 (mpt180) REVERT: B 277 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: B 376 ASP cc_start: 0.8261 (t0) cc_final: 0.7912 (t0) REVERT: B 380 TRP cc_start: 0.8313 (t-100) cc_final: 0.8087 (t-100) REVERT: C 118 ARG cc_start: 0.8644 (ptm160) cc_final: 0.8292 (ptm-80) REVERT: C 152 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7063 (mtm-85) REVERT: C 198 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7605 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7278 (ttt180) cc_final: 0.6144 (mpt180) REVERT: C 277 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: C 376 ASP cc_start: 0.8250 (t0) cc_final: 0.7898 (t0) REVERT: C 380 TRP cc_start: 0.8308 (t-100) cc_final: 0.8085 (t-100) REVERT: D 118 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8291 (ptm-80) REVERT: D 152 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: D 198 PRO cc_start: 0.7803 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7275 (ttt180) cc_final: 0.6169 (mpt180) REVERT: D 273 ASN cc_start: 0.7718 (m-40) cc_final: 0.7422 (p0) REVERT: D 376 ASP cc_start: 0.8232 (t0) cc_final: 0.7864 (t0) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 0.1307 time to fit residues: 31.4042 Evaluate side-chains 190 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 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 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 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: 3.9990 chunk 46 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117981 restraints weight = 11295.349| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.31 r_work: 0.3075 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10588 Z= 0.129 Angle : 0.497 3.887 14384 Z= 0.272 Chirality : 0.048 0.148 1572 Planarity : 0.005 0.037 1804 Dihedral : 5.878 55.786 1576 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.32 % Favored : 98.37 % Rotamer: Outliers : 2.66 % Allowed : 14.10 % Favored : 83.24 % 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: -0.07 (0.23), residues: 1288 helix: -3.14 (0.20), residues: 24 sheet: 0.21 (0.21), residues: 564 loop : -0.03 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 156 TYR 0.007 0.001 TYR A 316 PHE 0.015 0.002 PHE C 121 TRP 0.013 0.001 TRP A 179 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00314 (10548) covalent geometry : angle 0.49259 (14296) SS BOND : bond 0.00143 ( 32) SS BOND : angle 0.84174 ( 64) hydrogen bonds : bond 0.03633 ( 352) hydrogen bonds : angle 6.10015 ( 936) link_NAG-ASN : bond 0.00093 ( 8) link_NAG-ASN : angle 1.27001 ( 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 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8714 (ptm160) cc_final: 0.8376 (ptm-80) REVERT: A 152 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7172 (mtm-85) REVERT: A 198 PRO cc_start: 0.7832 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6150 (mpt180) REVERT: A 277 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: A 376 ASP cc_start: 0.8151 (t0) cc_final: 0.7836 (t0) REVERT: B 118 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8364 (ptm-80) REVERT: B 198 PRO cc_start: 0.7807 (Cg_exo) cc_final: 0.7584 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6143 (mpt180) REVERT: B 277 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: B 376 ASP cc_start: 0.8173 (t0) cc_final: 0.7839 (t0) REVERT: C 118 ARG cc_start: 0.8662 (ptm160) cc_final: 0.8334 (ptm-80) REVERT: C 152 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: C 198 PRO cc_start: 0.7816 (Cg_exo) cc_final: 0.7583 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6136 (mpt180) REVERT: C 277 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: C 376 ASP cc_start: 0.8179 (t0) cc_final: 0.7840 (t0) REVERT: D 118 ARG cc_start: 0.8673 (ptm160) cc_final: 0.8353 (ptm-80) REVERT: D 152 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: D 198 PRO cc_start: 0.7790 (Cg_exo) cc_final: 0.7563 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7231 (ttt180) cc_final: 0.6130 (mpt180) REVERT: D 273 ASN cc_start: 0.7682 (m-40) cc_final: 0.7408 (p0) REVERT: D 376 ASP cc_start: 0.8164 (t0) cc_final: 0.7808 (t0) outliers start: 30 outliers final: 26 residues processed: 182 average time/residue: 0.1319 time to fit residues: 31.8361 Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 277 GLU 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 102 optimal weight: 0.0870 chunk 104 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.119596 restraints weight = 11429.601| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.32 r_work: 0.3112 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4400 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= 0.108 Angle : 0.476 3.761 14384 Z= 0.261 Chirality : 0.047 0.147 1572 Planarity : 0.004 0.038 1804 Dihedral : 5.750 55.175 1576 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.02 % Favored : 97.67 % Rotamer: Outliers : 1.86 % Allowed : 15.60 % 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: 0.08 (0.23), residues: 1288 helix: -2.82 (0.26), residues: 24 sheet: 0.31 (0.21), residues: 564 loop : 0.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.007 0.001 TYR B 316 PHE 0.013 0.002 PHE D 121 TRP 0.014 0.001 TRP B 179 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00256 (10548) covalent geometry : angle 0.47206 (14296) SS BOND : bond 0.00136 ( 32) SS BOND : angle 0.79087 ( 64) hydrogen bonds : bond 0.03403 ( 352) hydrogen bonds : angle 5.94005 ( 936) link_NAG-ASN : bond 0.00125 ( 8) link_NAG-ASN : angle 1.17895 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.65 seconds wall clock time: 43 minutes 38.15 seconds (2618.15 seconds total)