Starting phenix.real_space_refine on Mon Jul 28 11:51:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_26319.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_26319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_26319.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_26319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2t_26319/07_2025/7u2t_26319.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} 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: C, B, D Time building chain proxies: 5.15, per 1000 atoms: 0.50 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 C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.05 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.07 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.07 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.07 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.05 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.44 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: 3.11 Time building geometry restraints manager: 2.90 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.005 TRP B 179 HIS 0.003 0.002 HIS D 275 PHE 0.021 0.004 PHE D 406 TYR 0.033 0.005 TYR D 276 ARG 0.005 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.02616 ( 8) link_NAG-ASN : angle 6.44533 ( 24) hydrogen bonds : bond 0.19215 ( 352) hydrogen bonds : angle 8.22711 ( 936) SS BOND : bond 0.01788 ( 32) SS BOND : angle 4.35737 ( 64) covalent geometry : bond 0.01353 (10548) covalent geometry : angle 1.54221 (14296) *********************** 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 : 1.112 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: 0.2721 time to fit residues: 112.5852 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 : 1.079 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS B 185 HIS B 189 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS C 131 GLN C 185 HIS C 189 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 131 GLN D 185 HIS D 189 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.127829 restraints weight = 11084.451| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.13 r_work: 0.3242 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10588 Z= 0.153 Angle : 0.590 3.840 14384 Z= 0.325 Chirality : 0.049 0.148 1572 Planarity : 0.005 0.034 1804 Dihedral : 7.178 58.223 1588 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 2.39 % Allowed : 8.87 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1288 helix: -2.57 (0.28), residues: 24 sheet: 0.72 (0.21), residues: 544 loop : 0.21 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 179 HIS 0.006 0.003 HIS D 275 PHE 0.019 0.002 PHE C 406 TYR 0.010 0.001 TYR A 316 ARG 0.004 0.001 ARG D 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 8) link_NAG-ASN : angle 1.73824 ( 24) hydrogen bonds : bond 0.04533 ( 352) hydrogen bonds : angle 6.62701 ( 936) SS BOND : bond 0.00204 ( 32) SS BOND : angle 0.94171 ( 64) covalent geometry : bond 0.00352 (10548) covalent geometry : angle 0.58386 (14296) *********************** 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: 27 poor density : 186 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6331 (mpt180) REVERT: A 361 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.7212 (ptm-80) REVERT: A 390 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7683 (ttmm) REVERT: B 220 ARG cc_start: 0.7006 (ttt180) cc_final: 0.6332 (mpt180) REVERT: B 361 ARG cc_start: 0.7471 (ptm-80) cc_final: 0.7178 (ptm-80) REVERT: B 390 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7692 (ttmm) REVERT: C 220 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6321 (mpt180) REVERT: C 361 ARG cc_start: 0.7513 (ptm-80) cc_final: 0.7206 (ptm-80) REVERT: C 390 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7688 (ttmm) REVERT: D 220 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6341 (mpt180) REVERT: D 361 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7189 (ptm-80) REVERT: D 390 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7690 (ttmm) outliers start: 27 outliers final: 23 residues processed: 209 average time/residue: 0.2436 time to fit residues: 70.0189 Evaluate side-chains 182 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 A residue 452 THR 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 B residue 452 THR 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 C residue 452 THR 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 Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.8980 chunk 106 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 275 HIS B 185 HIS B 275 HIS C 185 HIS C 275 HIS D 131 GLN D 185 HIS D 275 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.154991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.125590 restraints weight = 11396.026| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.23 r_work: 0.3179 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10588 Z= 0.116 Angle : 0.503 3.526 14384 Z= 0.279 Chirality : 0.047 0.141 1572 Planarity : 0.004 0.040 1804 Dihedral : 6.027 55.689 1580 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.93 % Favored : 98.76 % Rotamer: Outliers : 2.22 % Allowed : 10.28 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1288 helix: -2.79 (0.28), residues: 24 sheet: 0.92 (0.22), residues: 528 loop : 0.19 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.005 0.002 HIS B 275 PHE 0.014 0.002 PHE A 121 TYR 0.006 0.001 TYR C 316 ARG 0.003 0.000 ARG D 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 8) link_NAG-ASN : angle 1.12665 ( 24) hydrogen bonds : bond 0.03913 ( 352) hydrogen bonds : angle 6.27476 ( 936) SS BOND : bond 0.00222 ( 32) SS BOND : angle 0.83204 ( 64) covalent geometry : bond 0.00271 (10548) covalent geometry : angle 0.49924 (14296) *********************** 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 192 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8210 (ptm-80) REVERT: A 220 ARG cc_start: 0.7112 (ttt180) cc_final: 0.6410 (mpt180) REVERT: B 118 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8193 (ptm-80) REVERT: B 220 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6402 (mpt180) REVERT: C 118 ARG cc_start: 0.8489 (ptm160) cc_final: 0.8199 (ptm-80) REVERT: C 220 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6393 (mpt180) REVERT: C 390 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8123 (ttpt) REVERT: D 118 ARG cc_start: 0.8481 (ptm160) cc_final: 0.8199 (ptm-80) REVERT: D 220 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6431 (mpt180) outliers start: 25 outliers final: 17 residues processed: 184 average time/residue: 0.2745 time to fit residues: 67.9193 Evaluate side-chains 162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 ASP 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 392 ASP 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 392 ASP 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 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 275 HIS B 185 HIS B 275 HIS C 185 HIS C 275 HIS D 185 HIS D 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122628 restraints weight = 11402.750| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.05 r_work: 0.3142 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10588 Z= 0.170 Angle : 0.528 3.869 14384 Z= 0.289 Chirality : 0.048 0.150 1572 Planarity : 0.005 0.041 1804 Dihedral : 5.946 55.960 1576 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.01 % Favored : 98.68 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1288 helix: -3.08 (0.23), residues: 24 sheet: 0.56 (0.21), residues: 548 loop : 0.05 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 179 HIS 0.006 0.003 HIS A 275 PHE 0.017 0.002 PHE D 406 TYR 0.007 0.001 TYR A 274 ARG 0.006 0.001 ARG C 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 1.15600 ( 24) hydrogen bonds : bond 0.04116 ( 352) hydrogen bonds : angle 6.19750 ( 936) SS BOND : bond 0.00184 ( 32) SS BOND : angle 0.95534 ( 64) covalent geometry : bond 0.00417 (10548) covalent geometry : angle 0.52325 (14296) *********************** 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 189 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8623 (ptm160) cc_final: 0.8269 (ptm-80) REVERT: A 220 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6488 (mpt180) REVERT: A 265 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7878 (tptp) REVERT: A 380 TRP cc_start: 0.8429 (t-100) cc_final: 0.8154 (t-100) REVERT: B 118 ARG cc_start: 0.8617 (ptm160) cc_final: 0.8264 (ptm-80) REVERT: B 220 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6478 (mpt180) REVERT: B 265 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7880 (tptp) REVERT: B 380 TRP cc_start: 0.8430 (t-100) cc_final: 0.8155 (t-100) REVERT: C 118 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8325 (ptm-80) REVERT: C 220 ARG cc_start: 0.7176 (ttt180) cc_final: 0.6488 (mpt180) REVERT: C 265 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (tptp) REVERT: C 380 TRP cc_start: 0.8421 (t-100) cc_final: 0.8151 (t-100) REVERT: D 118 ARG cc_start: 0.8633 (ptm160) cc_final: 0.8332 (ptm-80) REVERT: D 220 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6481 (mpt180) REVERT: D 265 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7876 (tptp) REVERT: D 380 TRP cc_start: 0.8422 (t-100) cc_final: 0.8151 (t-100) outliers start: 28 outliers final: 20 residues processed: 177 average time/residue: 0.3639 time to fit residues: 87.8264 Evaluate side-chains 173 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 227 GLN A 275 HIS B 185 HIS B 227 GLN B 275 HIS C 185 HIS C 227 GLN C 275 HIS D 185 HIS D 227 GLN D 275 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.147589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117170 restraints weight = 11547.770| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.31 r_work: 0.3086 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10588 Z= 0.229 Angle : 0.566 4.178 14384 Z= 0.307 Chirality : 0.049 0.151 1572 Planarity : 0.005 0.040 1804 Dihedral : 6.068 57.065 1576 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.25 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 11.79 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1288 helix: -3.25 (0.20), residues: 24 sheet: 0.29 (0.21), residues: 548 loop : -0.20 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 179 HIS 0.006 0.002 HIS B 275 PHE 0.020 0.003 PHE C 406 TYR 0.007 0.001 TYR C 316 ARG 0.005 0.001 ARG D 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 8) link_NAG-ASN : angle 1.33418 ( 24) hydrogen bonds : bond 0.04316 ( 352) hydrogen bonds : angle 6.30570 ( 936) SS BOND : bond 0.00191 ( 32) SS BOND : angle 1.04775 ( 64) covalent geometry : bond 0.00570 (10548) covalent geometry : angle 0.56059 (14296) *********************** 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 174 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8307 (ptm-80) REVERT: A 220 ARG cc_start: 0.6991 (ttt180) cc_final: 0.6285 (mpt180) REVERT: A 265 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (tptp) REVERT: A 275 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7517 (m-70) REVERT: A 376 ASP cc_start: 0.7866 (t0) cc_final: 0.7500 (t0) REVERT: A 380 TRP cc_start: 0.8427 (t-100) cc_final: 0.8191 (t-100) REVERT: B 118 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8308 (ptm-80) REVERT: B 220 ARG cc_start: 0.6977 (ttt180) cc_final: 0.6285 (mpt180) REVERT: B 265 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7831 (tptp) REVERT: B 275 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7525 (m-70) REVERT: B 376 ASP cc_start: 0.7883 (t0) cc_final: 0.7523 (t0) REVERT: B 380 TRP cc_start: 0.8422 (t-100) cc_final: 0.8188 (t-100) REVERT: C 118 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8355 (ptm-80) REVERT: C 220 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6289 (mpt180) REVERT: C 265 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7826 (tptp) REVERT: C 275 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7526 (m-70) REVERT: C 376 ASP cc_start: 0.7868 (t0) cc_final: 0.7501 (t0) REVERT: C 380 TRP cc_start: 0.8415 (t-100) cc_final: 0.8183 (t-100) REVERT: D 118 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8359 (ptm-80) REVERT: D 220 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6301 (mpt180) REVERT: D 265 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7832 (tptp) REVERT: D 275 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7517 (m-70) REVERT: D 376 ASP cc_start: 0.7855 (t0) cc_final: 0.7485 (t0) REVERT: D 380 TRP cc_start: 0.8418 (t-100) cc_final: 0.8184 (t-100) outliers start: 28 outliers final: 16 residues processed: 162 average time/residue: 0.3122 time to fit residues: 68.1154 Evaluate side-chains 168 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.149920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118439 restraints weight = 11456.589| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.41 r_work: 0.3108 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3612 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= 0.123 Angle : 0.484 3.819 14384 Z= 0.266 Chirality : 0.047 0.145 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.821 55.161 1576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.09 % Favored : 98.60 % Rotamer: Outliers : 2.39 % Allowed : 11.35 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1288 helix: -2.99 (0.25), residues: 24 sheet: 0.37 (0.22), residues: 520 loop : -0.22 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.002 0.001 HIS C 185 PHE 0.014 0.002 PHE A 406 TYR 0.007 0.001 TYR C 276 ARG 0.004 0.001 ARG D 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 8) link_NAG-ASN : angle 1.18366 ( 24) hydrogen bonds : bond 0.03603 ( 352) hydrogen bonds : angle 6.14029 ( 936) SS BOND : bond 0.00154 ( 32) SS BOND : angle 0.83775 ( 64) covalent geometry : bond 0.00295 (10548) covalent geometry : angle 0.47987 (14296) *********************** 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 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8351 (ptm-80) REVERT: A 220 ARG cc_start: 0.6978 (ttt180) cc_final: 0.6262 (mpt180) REVERT: A 265 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7662 (tptp) REVERT: A 275 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7674 (t-170) REVERT: A 376 ASP cc_start: 0.7822 (t0) cc_final: 0.7473 (t0) REVERT: B 118 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8329 (ptm-80) REVERT: B 220 ARG cc_start: 0.6971 (ttt180) cc_final: 0.6253 (mpt180) REVERT: B 275 HIS cc_start: 0.8357 (t70) cc_final: 0.7551 (t-170) REVERT: B 376 ASP cc_start: 0.7842 (t0) cc_final: 0.7497 (t0) REVERT: C 118 ARG cc_start: 0.8674 (ptm160) cc_final: 0.8342 (ptm-80) REVERT: C 220 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6257 (mpt180) REVERT: C 265 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7649 (tptp) REVERT: C 275 HIS cc_start: 0.8407 (t70) cc_final: 0.7618 (t-170) REVERT: C 376 ASP cc_start: 0.7819 (t0) cc_final: 0.7474 (t0) REVERT: D 118 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8342 (ptm-80) REVERT: D 220 ARG cc_start: 0.6985 (ttt180) cc_final: 0.6270 (mpt180) REVERT: D 275 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7673 (t-170) REVERT: D 376 ASP cc_start: 0.7810 (t0) cc_final: 0.7456 (t0) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.2490 time to fit residues: 59.0330 Evaluate side-chains 170 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 392 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119564 restraints weight = 11545.280| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.34 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3718 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= 0.116 Angle : 0.478 3.796 14384 Z= 0.261 Chirality : 0.047 0.144 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.764 54.858 1576 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.32 % Favored : 98.37 % Rotamer: Outliers : 2.22 % Allowed : 12.06 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1288 helix: -2.97 (0.24), residues: 24 sheet: 0.32 (0.22), residues: 520 loop : -0.18 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 179 HIS 0.003 0.001 HIS C 275 PHE 0.014 0.002 PHE D 121 TYR 0.010 0.001 TYR A 274 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 8) link_NAG-ASN : angle 1.09155 ( 24) hydrogen bonds : bond 0.03479 ( 352) hydrogen bonds : angle 6.05273 ( 936) SS BOND : bond 0.00153 ( 32) SS BOND : angle 0.82606 ( 64) covalent geometry : bond 0.00280 (10548) covalent geometry : angle 0.47461 (14296) *********************** 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 182 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8719 (ptm160) cc_final: 0.8379 (ptm-80) REVERT: A 220 ARG cc_start: 0.6963 (ttt180) cc_final: 0.6228 (mpt180) REVERT: A 277 GLU cc_start: 0.8548 (mp0) cc_final: 0.8188 (mp0) REVERT: A 376 ASP cc_start: 0.7836 (t0) cc_final: 0.7492 (t0) REVERT: B 118 ARG cc_start: 0.8739 (ptm160) cc_final: 0.8396 (ptm-80) REVERT: B 198 PRO cc_start: 0.7711 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: B 220 ARG cc_start: 0.6963 (ttt180) cc_final: 0.6222 (mpt180) REVERT: B 376 ASP cc_start: 0.7865 (t0) cc_final: 0.7520 (t0) REVERT: C 118 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8353 (ptm-80) REVERT: C 198 PRO cc_start: 0.7710 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: C 220 ARG cc_start: 0.6958 (ttt180) cc_final: 0.6218 (mpt180) REVERT: C 376 ASP cc_start: 0.7853 (t0) cc_final: 0.7514 (t0) REVERT: D 118 ARG cc_start: 0.8668 (ptm160) cc_final: 0.8353 (ptm-80) REVERT: D 198 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: D 220 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6263 (mpt180) REVERT: D 277 GLU cc_start: 0.8555 (mp0) cc_final: 0.8196 (mp0) REVERT: D 376 ASP cc_start: 0.7835 (t0) cc_final: 0.7488 (t0) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 0.4446 time to fit residues: 109.4186 Evaluate side-chains 165 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 CYS 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 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 231 CYS 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 29 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.114299 restraints weight = 11559.653| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.40 r_work: 0.3026 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3969 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= 0.237 Angle : 0.571 4.447 14384 Z= 0.307 Chirality : 0.050 0.157 1572 Planarity : 0.005 0.038 1804 Dihedral : 6.142 57.901 1576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.87 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 12.06 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1288 helix: -3.36 (0.18), residues: 24 sheet: 0.11 (0.21), residues: 556 loop : -0.15 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 179 HIS 0.004 0.002 HIS D 275 PHE 0.020 0.003 PHE C 406 TYR 0.010 0.001 TYR D 274 ARG 0.007 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.41173 ( 24) hydrogen bonds : bond 0.04285 ( 352) hydrogen bonds : angle 6.32467 ( 936) SS BOND : bond 0.00211 ( 32) SS BOND : angle 1.05814 ( 64) covalent geometry : bond 0.00588 (10548) covalent geometry : angle 0.56535 (14296) *********************** 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 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8701 (ptm160) cc_final: 0.8339 (ptm-80) REVERT: A 220 ARG cc_start: 0.7138 (ttt180) cc_final: 0.6108 (mpt180) REVERT: A 376 ASP cc_start: 0.8182 (t0) cc_final: 0.7828 (t0) REVERT: B 118 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8331 (ptm-80) REVERT: B 220 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6108 (mpt180) REVERT: B 376 ASP cc_start: 0.8195 (t0) cc_final: 0.7851 (t0) REVERT: C 118 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8311 (ptm-80) REVERT: C 220 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6090 (mpt180) REVERT: C 376 ASP cc_start: 0.8194 (t0) cc_final: 0.7844 (t0) REVERT: D 118 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8322 (ptm-80) REVERT: D 220 ARG cc_start: 0.6957 (ttt180) cc_final: 0.6192 (mpt180) REVERT: D 376 ASP cc_start: 0.8188 (t0) cc_final: 0.7837 (t0) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.2488 time to fit residues: 59.8443 Evaluate side-chains 170 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 243 THR 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 243 THR 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 243 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 275 HIS C 136 GLN D 136 GLN D 273 ASN D 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116959 restraints weight = 11520.913| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.36 r_work: 0.3069 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10588 Z= 0.150 Angle : 0.513 3.886 14384 Z= 0.280 Chirality : 0.048 0.164 1572 Planarity : 0.005 0.039 1804 Dihedral : 5.978 56.289 1576 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.33 % Favored : 97.36 % Rotamer: Outliers : 2.84 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1288 helix: -3.20 (0.21), residues: 24 sheet: 0.18 (0.22), residues: 528 loop : -0.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 179 HIS 0.004 0.002 HIS D 275 PHE 0.016 0.002 PHE D 121 TYR 0.010 0.001 TYR A 253 ARG 0.006 0.001 ARG D 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 8) link_NAG-ASN : angle 1.30052 ( 24) hydrogen bonds : bond 0.03752 ( 352) hydrogen bonds : angle 6.22548 ( 936) SS BOND : bond 0.00160 ( 32) SS BOND : angle 0.89004 ( 64) covalent geometry : bond 0.00368 (10548) covalent geometry : angle 0.50833 (14296) *********************** 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 193 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8696 (ptm160) cc_final: 0.8354 (ptm-80) REVERT: A 152 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: A 220 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6124 (mpt180) REVERT: A 376 ASP cc_start: 0.8173 (t0) cc_final: 0.7820 (t0) REVERT: B 118 ARG cc_start: 0.8683 (ptm160) cc_final: 0.8333 (ptm-80) REVERT: B 152 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: B 198 PRO cc_start: 0.7855 (Cg_exo) cc_final: 0.7557 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7198 (ttt180) cc_final: 0.6167 (mpt180) REVERT: B 376 ASP cc_start: 0.8171 (t0) cc_final: 0.7826 (t0) REVERT: C 118 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8297 (ptm-80) REVERT: C 152 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.7114 (mtm-85) REVERT: C 198 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7543 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7154 (ttt180) cc_final: 0.6134 (mpt180) REVERT: C 376 ASP cc_start: 0.8174 (t0) cc_final: 0.7829 (t0) REVERT: D 118 ARG cc_start: 0.8654 (ptm160) cc_final: 0.8322 (ptm-80) REVERT: D 152 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7203 (mtm-85) REVERT: D 198 PRO cc_start: 0.7840 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7146 (ttt180) cc_final: 0.6112 (mpt180) REVERT: D 376 ASP cc_start: 0.8188 (t0) cc_final: 0.7842 (t0) outliers start: 32 outliers final: 26 residues processed: 180 average time/residue: 0.2790 time to fit residues: 67.2413 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 : 1.212 ------------------------------------------------------------------------------- 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 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 243 THR 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 28 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.150099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117776 restraints weight = 11433.233| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.46 r_work: 0.3114 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4169 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= 0.115 Angle : 0.494 3.814 14384 Z= 0.270 Chirality : 0.048 0.161 1572 Planarity : 0.005 0.040 1804 Dihedral : 5.845 55.247 1576 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.41 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 13.83 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1288 helix: -2.95 (0.26), residues: 24 sheet: 0.26 (0.22), residues: 528 loop : -0.14 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 179 HIS 0.004 0.001 HIS C 275 PHE 0.013 0.002 PHE D 121 TYR 0.011 0.001 TYR D 253 ARG 0.006 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 8) link_NAG-ASN : angle 1.22131 ( 24) hydrogen bonds : bond 0.03480 ( 352) hydrogen bonds : angle 6.08682 ( 936) SS BOND : bond 0.00139 ( 32) SS BOND : angle 0.81749 ( 64) covalent geometry : bond 0.00274 (10548) covalent geometry : angle 0.49030 (14296) ********************** 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 186 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8738 (ptm160) cc_final: 0.8400 (ptm-80) REVERT: A 198 PRO cc_start: 0.7882 (Cg_exo) cc_final: 0.7589 (Cg_endo) REVERT: A 220 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6163 (mpt180) REVERT: A 275 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7467 (t-170) REVERT: A 376 ASP cc_start: 0.8172 (t0) cc_final: 0.7835 (t0) REVERT: B 118 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8396 (ptm-80) REVERT: B 198 PRO cc_start: 0.7880 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: B 220 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6173 (mpt180) REVERT: B 376 ASP cc_start: 0.8170 (t0) cc_final: 0.7838 (t0) REVERT: C 118 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8327 (ptm-80) REVERT: C 198 PRO cc_start: 0.7861 (Cg_exo) cc_final: 0.7562 (Cg_endo) REVERT: C 220 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6165 (mpt180) REVERT: C 376 ASP cc_start: 0.8170 (t0) cc_final: 0.7839 (t0) REVERT: D 118 ARG cc_start: 0.8653 (ptm160) cc_final: 0.8351 (ptm-80) REVERT: D 198 PRO cc_start: 0.7866 (Cg_exo) cc_final: 0.7577 (Cg_endo) REVERT: D 220 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6148 (mpt180) REVERT: D 376 ASP cc_start: 0.8181 (t0) cc_final: 0.7846 (t0) outliers start: 26 outliers final: 23 residues processed: 172 average time/residue: 0.3679 time to fit residues: 86.5850 Evaluate side-chains 168 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 243 THR Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 0.0470 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN C 273 ASN D 275 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119779 restraints weight = 11365.580| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.44 r_work: 0.3144 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10588 Z= 0.098 Angle : 0.476 3.714 14384 Z= 0.261 Chirality : 0.047 0.159 1572 Planarity : 0.005 0.040 1804 Dihedral : 5.763 54.847 1576 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.94 % Favored : 97.75 % Rotamer: Outliers : 2.04 % Allowed : 14.54 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1288 helix: -2.82 (0.28), residues: 24 sheet: 0.28 (0.22), residues: 528 loop : -0.09 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.013 0.002 HIS A 275 PHE 0.013 0.002 PHE D 121 TYR 0.012 0.001 TYR A 316 ARG 0.006 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 8) link_NAG-ASN : angle 1.12846 ( 24) hydrogen bonds : bond 0.03299 ( 352) hydrogen bonds : angle 5.98393 ( 936) SS BOND : bond 0.00135 ( 32) SS BOND : angle 0.77430 ( 64) covalent geometry : bond 0.00226 (10548) covalent geometry : angle 0.47193 (14296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.77 seconds wall clock time: 105 minutes 2.55 seconds (6302.55 seconds total)