Starting phenix.real_space_refine on Fri Jul 3 18:53:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.map" model { file = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upb_26660/07_2026/7upb_26660.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 90 5.16 5 C 9918 2.51 5 N 2580 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15654 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3454 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 16, 'TRANS': 432} Chain: "B" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3454 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 16, 'TRANS': 432} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3454 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 16, 'TRANS': 432} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.50, per 1000 atoms: 0.22 Number of scatterers: 15654 At special positions: 0 Unit cell: (156.04, 171.08, 112.8, 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 90 16.00 O 3066 8.00 N 2580 7.00 C 9918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 414 " " NAG D 501 " - " ASN D 414 " " NAG G 501 " - " ASN G 414 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 681.9 milliseconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3750 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 27.7% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 65 through 72 removed outlier: 4.006A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.597A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.146A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.565A pdb=" N LEU A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.117A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.776A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 475 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.644A pdb=" N SER B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.652A pdb=" N SER C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 36 Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.510A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.586A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.582A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 146 removed outlier: 4.110A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.074A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.775A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 452 through 475 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.683A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.651A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.500A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.568A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 146 removed outlier: 4.104A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 183 removed outlier: 3.583A pdb=" N LEU G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 4.086A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.786A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 452 through 475 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.645A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.647A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 10.233A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.965A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.112A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.687A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.590A pdb=" N ILE B 34 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.590A pdb=" N ILE C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 162 removed outlier: 10.245A pdb=" N THR D 168 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP D 56 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.028A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AB5, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB7, first strand: chain 'D' and resid 393 through 394 removed outlier: 6.759A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.535A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.542A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN F 50 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 158 through 162 removed outlier: 10.247A pdb=" N THR G 168 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP G 56 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU G 38 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 296 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LYS G 40 " --> pdb=" O GLN G 294 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N GLN G 294 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N VAL G 42 " --> pdb=" O TYR G 292 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N TYR G 292 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 11.525A pdb=" N ARG G 44 " --> pdb=" O GLN G 290 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLN G 290 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR G 46 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 333 Processing sheet with id=AC4, first strand: chain 'G' and resid 226 through 227 removed outlier: 3.993A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR G 46 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLN G 290 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 11.525A pdb=" N ARG G 44 " --> pdb=" O GLN G 290 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N TYR G 292 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N VAL G 42 " --> pdb=" O TYR G 292 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N GLN G 294 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LYS G 40 " --> pdb=" O GLN G 294 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 296 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU G 38 " --> pdb=" O LEU G 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AC5, first strand: chain 'G' and resid 301 through 302 removed outlier: 6.113A pdb=" N ARG G 365 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.585A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN L 50 " --> pdb=" O THR L 53 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1695 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: 3.17 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5029 1.34 - 1.46: 3200 1.46 - 1.58: 7587 1.58 - 1.70: 0 1.70 - 1.81: 132 Bond restraints: 15948 Sorted by residual: bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" CG LEU G 409 " pdb=" CD1 LEU G 409 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" N PHE F 91 " pdb=" CA PHE F 91 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.65e+00 ... (remaining 15943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 21530 2.78 - 5.57: 112 5.57 - 8.35: 4 8.35 - 11.14: 0 11.14 - 13.92: 2 Bond angle restraints: 21648 Sorted by residual: angle pdb=" CA LEU A 147 " pdb=" CB LEU A 147 " pdb=" CG LEU A 147 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" CA LEU D 147 " pdb=" CB LEU D 147 " pdb=" CG LEU D 147 " ideal model delta sigma weight residual 116.30 129.64 -13.34 3.50e+00 8.16e-02 1.45e+01 angle pdb=" N VAL A 108 " pdb=" CA VAL A 108 " pdb=" C VAL A 108 " ideal model delta sigma weight residual 111.77 108.38 3.39 1.04e+00 9.25e-01 1.06e+01 angle pdb=" N VAL D 108 " pdb=" CA VAL D 108 " pdb=" C VAL D 108 " ideal model delta sigma weight residual 111.91 109.25 2.66 8.90e-01 1.26e+00 8.92e+00 angle pdb=" N VAL G 108 " pdb=" CA VAL G 108 " pdb=" C VAL G 108 " ideal model delta sigma weight residual 111.91 109.27 2.64 8.90e-01 1.26e+00 8.77e+00 ... (remaining 21643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 8649 17.53 - 35.06: 707 35.06 - 52.58: 197 52.58 - 70.11: 36 70.11 - 87.64: 11 Dihedral angle restraints: 9600 sinusoidal: 3738 harmonic: 5862 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -145.85 59.85 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -137.72 51.72 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CB CYS G 71 " pdb=" SG CYS G 71 " pdb=" SG CYS G 192 " pdb=" CB CYS G 192 " ideal model delta sinusoidal sigma weight residual -86.00 -136.20 50.20 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 9597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1686 0.037 - 0.074: 567 0.074 - 0.111: 178 0.111 - 0.148: 79 0.148 - 0.185: 10 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 414 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA PHE F 91 " pdb=" N PHE F 91 " pdb=" C PHE F 91 " pdb=" CB PHE F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 2517 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 79 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO F 80 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 80 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO L 80 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 79 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO E 80 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 80 " 0.021 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2073 2.76 - 3.29: 14237 3.29 - 3.83: 25818 3.83 - 4.36: 31392 4.36 - 4.90: 55391 Nonbonded interactions: 128911 Sorted by model distance: nonbonded pdb=" OG1 THR G 334 " pdb=" O SER G 337 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR D 334 " pdb=" O SER D 337 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR L 22 " pdb=" OE1 GLN L 70 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.308 3.040 ... (remaining 128906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } 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: 7.740 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:9.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15975 Z= 0.148 Angle : 0.569 13.925 21705 Z= 0.303 Chirality : 0.046 0.185 2520 Planarity : 0.004 0.038 2751 Dihedral : 14.207 87.639 5778 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.68 % Allowed : 10.69 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2007 helix: 1.05 (0.24), residues: 444 sheet: 0.54 (0.21), residues: 618 loop : -0.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 244 TYR 0.019 0.001 TYR E 49 PHE 0.026 0.001 PHE F 91 TRP 0.019 0.002 TRP F 92 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15948) covalent geometry : angle 0.56357 / 0.30 (21648) SS BOND : bond 0.00295 / 0.18 ( 24) SS BOND : angle 0.71855 / 0.46 ( 48) hydrogen bonds : bond 0.14389 / 8.89 ( 626) hydrogen bonds : angle 6.50308 / 4.62 ( 1695) link_NAG-ASN : bond 0.00781 / 0.38 ( 3) link_NAG-ASN : angle 3.83897 / 1.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 MET cc_start: 0.9256 (mmm) cc_final: 0.8866 (mtt) outliers start: 12 outliers final: 8 residues processed: 164 average time/residue: 0.4490 time to fit residues: 83.6463 Evaluate side-chains 163 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 421 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN G 350 ASN H 76 ASN L 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106729 restraints weight = 18521.498| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.08 r_work: 0.3090 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15975 Z= 0.167 Angle : 0.542 11.587 21705 Z= 0.276 Chirality : 0.046 0.226 2520 Planarity : 0.004 0.031 2751 Dihedral : 4.678 50.381 2174 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.50 % Allowed : 9.67 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 2007 helix: 1.48 (0.25), residues: 450 sheet: 0.63 (0.21), residues: 612 loop : -0.19 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 375 TYR 0.021 0.001 TYR F 49 PHE 0.028 0.001 PHE F 91 TRP 0.016 0.002 TRP F 92 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (15948) covalent geometry : angle 0.53748 / 0.28 (21648) SS BOND : bond 0.00342 / 0.21 ( 24) SS BOND : angle 0.58246 / 0.37 ( 48) hydrogen bonds : bond 0.03638 / 2.38 ( 626) hydrogen bonds : angle 4.91991 / 3.49 ( 1695) link_NAG-ASN : bond 0.00658 / 0.31 ( 3) link_NAG-ASN : angle 3.55418 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8311 (m-80) cc_final: 0.8109 (m-80) REVERT: B 105 GLN cc_start: 0.8794 (pm20) cc_final: 0.8512 (pm20) REVERT: D 193 LYS cc_start: 0.8114 (tptt) cc_final: 0.7324 (tptp) REVERT: F 70 GLN cc_start: 0.8148 (pp30) cc_final: 0.7886 (pt0) REVERT: F 81 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7358 (pp20) REVERT: G 138 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6592 (mtp) REVERT: G 164 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6233 (p) outliers start: 44 outliers final: 25 residues processed: 195 average time/residue: 0.4122 time to fit residues: 91.0422 Evaluate side-chains 191 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 76 ASN D 424 ASN E 28 ASN F 38 GLN G 145 ASN H 76 ASN L 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105523 restraints weight = 18657.056| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.04 r_work: 0.3072 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15975 Z= 0.160 Angle : 0.524 11.466 21705 Z= 0.268 Chirality : 0.046 0.232 2520 Planarity : 0.004 0.033 2751 Dihedral : 4.643 56.147 2170 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.22 % Allowed : 10.86 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2007 helix: 1.66 (0.25), residues: 450 sheet: 0.58 (0.21), residues: 609 loop : -0.20 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 244 TYR 0.021 0.001 TYR F 49 PHE 0.027 0.001 PHE F 91 TRP 0.014 0.001 TRP F 92 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (15948) covalent geometry : angle 0.51930 / 0.27 (21648) SS BOND : bond 0.00354 / 0.22 ( 24) SS BOND : angle 0.56174 / 0.36 ( 48) hydrogen bonds : bond 0.03481 / 2.27 ( 626) hydrogen bonds : angle 4.72704 / 3.34 ( 1695) link_NAG-ASN : bond 0.00562 / 0.26 ( 3) link_NAG-ASN : angle 3.39108 / 1.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: A 416 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8741 (p) REVERT: B 97 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: B 105 GLN cc_start: 0.8793 (pm20) cc_final: 0.8519 (pm20) REVERT: F 70 GLN cc_start: 0.8108 (pp30) cc_final: 0.7851 (pt0) REVERT: F 81 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: G 138 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6512 (mtp) REVERT: G 164 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6273 (p) outliers start: 39 outliers final: 24 residues processed: 189 average time/residue: 0.3985 time to fit residues: 85.4451 Evaluate side-chains 185 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 424 ASN E 28 ASN H 76 ASN L 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106547 restraints weight = 18518.195| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.03 r_work: 0.3095 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15975 Z= 0.125 Angle : 0.489 10.991 21705 Z= 0.251 Chirality : 0.044 0.232 2520 Planarity : 0.003 0.031 2751 Dihedral : 4.511 58.968 2170 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.39 % Allowed : 11.09 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2007 helix: 1.88 (0.24), residues: 450 sheet: 0.60 (0.21), residues: 609 loop : -0.17 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.017 0.001 TYR F 49 PHE 0.025 0.001 PHE F 91 TRP 0.014 0.001 TRP F 92 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15948) covalent geometry : angle 0.48525 / 0.25 (21648) SS BOND : bond 0.00315 / 0.19 ( 24) SS BOND : angle 0.50113 / 0.33 ( 48) hydrogen bonds : bond 0.03104 / 2.03 ( 626) hydrogen bonds : angle 4.52550 / 3.20 ( 1695) link_NAG-ASN : bond 0.00562 / 0.27 ( 3) link_NAG-ASN : angle 3.13721 / 1.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: B 105 GLN cc_start: 0.8775 (pm20) cc_final: 0.8453 (pm20) REVERT: C 80 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8407 (ttm) REVERT: F 70 GLN cc_start: 0.8159 (pp30) cc_final: 0.7865 (pt0) REVERT: F 81 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: G 138 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6467 (mtp) REVERT: G 335 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7645 (pttp) outliers start: 42 outliers final: 25 residues processed: 187 average time/residue: 0.3980 time to fit residues: 84.8994 Evaluate side-chains 183 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN B 39 GLN B 76 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 424 ASN E 28 ASN E 38 GLN H 76 ASN L 28 ASN L 30 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109540 restraints weight = 18608.410| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.97 r_work: 0.3139 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15975 Z= 0.144 Angle : 0.506 11.024 21705 Z= 0.258 Chirality : 0.045 0.229 2520 Planarity : 0.003 0.031 2751 Dihedral : 4.552 58.509 2170 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.62 % Allowed : 11.38 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 2007 helix: 1.91 (0.24), residues: 450 sheet: 0.59 (0.21), residues: 609 loop : -0.22 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.020 0.001 TYR F 49 PHE 0.026 0.001 PHE F 91 TRP 0.015 0.001 TRP F 92 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 (15948) covalent geometry : angle 0.50157 / 0.26 (21648) SS BOND : bond 0.00331 / 0.20 ( 24) SS BOND : angle 0.50975 / 0.33 ( 48) hydrogen bonds : bond 0.03210 / 2.10 ( 626) hydrogen bonds : angle 4.52244 / 3.19 ( 1695) link_NAG-ASN : bond 0.00513 / 0.24 ( 3) link_NAG-ASN : angle 3.26651 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: A 416 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 105 GLN cc_start: 0.8776 (pm20) cc_final: 0.8467 (pm20) REVERT: F 61 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7376 (ttp80) REVERT: F 70 GLN cc_start: 0.8129 (pp30) cc_final: 0.7876 (pt0) REVERT: F 81 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7425 (pp20) REVERT: G 138 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6594 (mtp) REVERT: G 335 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7696 (pttp) REVERT: G 406 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7918 (pm20) outliers start: 46 outliers final: 30 residues processed: 189 average time/residue: 0.4162 time to fit residues: 89.5911 Evaluate side-chains 190 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 chunk 120 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN C 76 ASN D 424 ASN E 28 ASN H 76 ASN L 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111243 restraints weight = 18510.557| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.95 r_work: 0.3162 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15975 Z= 0.105 Angle : 0.466 10.504 21705 Z= 0.239 Chirality : 0.044 0.226 2520 Planarity : 0.003 0.032 2751 Dihedral : 4.361 56.064 2170 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.56 % Allowed : 11.49 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2007 helix: 2.09 (0.24), residues: 450 sheet: 0.64 (0.21), residues: 609 loop : -0.18 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.014 0.001 TYR E 49 PHE 0.023 0.001 PHE F 91 TRP 0.015 0.001 TRP F 92 HIS 0.002 0.000 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (15948) covalent geometry : angle 0.46236 / 0.24 (21648) SS BOND : bond 0.00287 / 0.18 ( 24) SS BOND : angle 0.47396 / 0.31 ( 48) hydrogen bonds : bond 0.02851 / 1.87 ( 626) hydrogen bonds : angle 4.36218 / 3.08 ( 1695) link_NAG-ASN : bond 0.00551 / 0.26 ( 3) link_NAG-ASN : angle 2.92382 / 1.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7943 (m-30) cc_final: 0.7703 (m-30) REVERT: A 406 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: A 416 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8803 (p) REVERT: B 105 GLN cc_start: 0.8785 (pm20) cc_final: 0.8457 (pm20) REVERT: F 61 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7247 (ttp80) REVERT: F 70 GLN cc_start: 0.8141 (pp30) cc_final: 0.7877 (pt0) REVERT: G 138 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6542 (mtp) REVERT: G 335 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7694 (pttp) outliers start: 45 outliers final: 25 residues processed: 198 average time/residue: 0.4381 time to fit residues: 98.7356 Evaluate side-chains 191 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 154 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 424 ASN B 76 ASN C 76 ASN E 28 ASN G 350 ASN H 39 GLN H 76 ASN L 28 ASN L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108112 restraints weight = 18385.401| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.90 r_work: 0.3123 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15975 Z= 0.193 Angle : 0.556 11.399 21705 Z= 0.282 Chirality : 0.047 0.224 2520 Planarity : 0.003 0.031 2751 Dihedral : 4.546 38.643 2168 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.45 % Allowed : 12.12 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 2007 helix: 1.84 (0.24), residues: 450 sheet: 0.55 (0.21), residues: 609 loop : -0.35 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.025 0.002 TYR E 49 PHE 0.029 0.002 PHE F 91 TRP 0.020 0.002 TRP F 92 HIS 0.006 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.19 (15948) covalent geometry : angle 0.55137 / 0.28 (21648) SS BOND : bond 0.00384 / 0.24 ( 24) SS BOND : angle 0.57375 / 0.38 ( 48) hydrogen bonds : bond 0.03556 / 2.34 ( 626) hydrogen bonds : angle 4.59922 / 3.24 ( 1695) link_NAG-ASN : bond 0.00419 / 0.19 ( 3) link_NAG-ASN : angle 3.61490 / 1.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: A 416 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8821 (p) REVERT: F 3 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: F 70 GLN cc_start: 0.8191 (pp30) cc_final: 0.7887 (pt0) REVERT: G 138 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6588 (mtp) REVERT: G 335 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7700 (pttp) outliers start: 43 outliers final: 31 residues processed: 190 average time/residue: 0.4340 time to fit residues: 93.7839 Evaluate side-chains 192 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 61 optimal weight: 0.0020 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN E 28 ASN G 424 ASN H 76 ASN L 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110700 restraints weight = 18626.419| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.97 r_work: 0.3156 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15975 Z= 0.103 Angle : 0.468 10.462 21705 Z= 0.240 Chirality : 0.044 0.219 2520 Planarity : 0.003 0.032 2751 Dihedral : 4.220 39.287 2168 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.28 % Allowed : 12.34 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2007 helix: 2.07 (0.25), residues: 450 sheet: 0.62 (0.21), residues: 609 loop : -0.27 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 244 TYR 0.012 0.001 TYR E 49 PHE 0.023 0.001 PHE F 91 TRP 0.014 0.001 TRP F 92 HIS 0.002 0.000 HIS L 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15948) covalent geometry : angle 0.46477 / 0.24 (21648) SS BOND : bond 0.00281 / 0.18 ( 24) SS BOND : angle 0.49251 / 0.33 ( 48) hydrogen bonds : bond 0.02842 / 1.86 ( 626) hydrogen bonds : angle 4.37062 / 3.08 ( 1695) link_NAG-ASN : bond 0.00536 / 0.26 ( 3) link_NAG-ASN : angle 2.90097 / 1.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7709 (pttp) REVERT: A 406 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 416 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8815 (p) REVERT: D 138 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6402 (mtp) REVERT: F 3 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: F 61 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7312 (ttp80) REVERT: F 70 GLN cc_start: 0.8172 (pp30) cc_final: 0.7861 (pt0) REVERT: G 61 MET cc_start: 0.9017 (mtt) cc_final: 0.8477 (mtt) REVERT: G 138 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6548 (mtp) REVERT: G 335 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7705 (pttp) REVERT: G 406 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7882 (pm20) outliers start: 40 outliers final: 25 residues processed: 191 average time/residue: 0.4277 time to fit residues: 93.1936 Evaluate side-chains 186 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN C 76 ASN D 424 ASN E 28 ASN G 350 ASN H 76 ASN L 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109844 restraints weight = 18585.215| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.96 r_work: 0.3145 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15975 Z= 0.124 Angle : 0.490 12.744 21705 Z= 0.249 Chirality : 0.044 0.224 2520 Planarity : 0.003 0.032 2751 Dihedral : 4.255 38.781 2168 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.10 % Allowed : 12.86 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2007 helix: 2.07 (0.25), residues: 450 sheet: 0.61 (0.21), residues: 609 loop : -0.30 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.016 0.001 TYR E 49 PHE 0.025 0.001 PHE F 91 TRP 0.016 0.001 TRP F 92 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (15948) covalent geometry : angle 0.48624 / 0.25 (21648) SS BOND : bond 0.00300 / 0.19 ( 24) SS BOND : angle 0.47848 / 0.32 ( 48) hydrogen bonds : bond 0.02995 / 1.96 ( 626) hydrogen bonds : angle 4.38669 / 3.09 ( 1695) link_NAG-ASN : bond 0.00500 / 0.23 ( 3) link_NAG-ASN : angle 3.09586 / 1.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7710 (pttp) REVERT: A 406 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: A 416 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (p) REVERT: F 3 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: F 61 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7285 (ttp80) REVERT: F 70 GLN cc_start: 0.8196 (pp30) cc_final: 0.7877 (pt0) REVERT: G 61 MET cc_start: 0.8988 (mtt) cc_final: 0.8468 (mtt) REVERT: G 138 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6564 (mtp) REVERT: G 335 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7719 (pttp) REVERT: G 406 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7866 (pm20) outliers start: 37 outliers final: 28 residues processed: 184 average time/residue: 0.4356 time to fit residues: 91.5594 Evaluate side-chains 189 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN C 76 ASN D 424 ASN E 28 ASN H 76 ASN L 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109374 restraints weight = 18500.449| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.91 r_work: 0.3138 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15975 Z= 0.151 Angle : 0.515 12.699 21705 Z= 0.261 Chirality : 0.045 0.223 2520 Planarity : 0.003 0.032 2751 Dihedral : 4.370 38.770 2168 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.16 % Allowed : 12.74 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2007 helix: 1.95 (0.24), residues: 450 sheet: 0.59 (0.22), residues: 603 loop : -0.34 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.019 0.001 TYR E 49 PHE 0.027 0.001 PHE F 91 TRP 0.020 0.001 TRP F 92 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (15948) covalent geometry : angle 0.51063 / 0.26 (21648) SS BOND : bond 0.00328 / 0.20 ( 24) SS BOND : angle 0.51879 / 0.35 ( 48) hydrogen bonds : bond 0.03205 / 2.10 ( 626) hydrogen bonds : angle 4.46553 / 3.15 ( 1695) link_NAG-ASN : bond 0.00458 / 0.21 ( 3) link_NAG-ASN : angle 3.26083 / 1.63 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7736 (pttp) REVERT: A 406 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: A 416 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8835 (p) REVERT: E 3 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: F 3 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: F 61 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7335 (ttp80) REVERT: F 70 GLN cc_start: 0.8224 (pp30) cc_final: 0.7906 (pt0) REVERT: G 61 MET cc_start: 0.8974 (mtt) cc_final: 0.8442 (mtt) REVERT: G 138 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6635 (mtp) REVERT: G 335 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7757 (pttp) REVERT: G 406 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: L 3 GLN cc_start: 0.8165 (mp10) cc_final: 0.7820 (pm20) outliers start: 38 outliers final: 27 residues processed: 183 average time/residue: 0.4284 time to fit residues: 89.4760 Evaluate side-chains 185 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 34 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN E 28 ASN G 350 ASN G 424 ASN H 76 ASN L 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110645 restraints weight = 18432.782| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.96 r_work: 0.3156 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15975 Z= 0.104 Angle : 0.472 11.916 21705 Z= 0.241 Chirality : 0.044 0.224 2520 Planarity : 0.003 0.032 2751 Dihedral : 4.193 39.060 2168 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.99 % Allowed : 12.97 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2007 helix: 2.11 (0.25), residues: 450 sheet: 0.61 (0.22), residues: 606 loop : -0.27 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.013 0.001 TYR E 49 PHE 0.023 0.001 PHE F 91 TRP 0.014 0.001 TRP F 92 HIS 0.002 0.000 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (15948) covalent geometry : angle 0.46852 / 0.24 (21648) SS BOND : bond 0.00274 / 0.17 ( 24) SS BOND : angle 0.47296 / 0.32 ( 48) hydrogen bonds : bond 0.02853 / 1.86 ( 626) hydrogen bonds : angle 4.35387 / 3.07 ( 1695) link_NAG-ASN : bond 0.00530 / 0.25 ( 3) link_NAG-ASN : angle 2.95117 / 1.48 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4905.33 seconds wall clock time: 84 minutes 32.04 seconds (5072.04 seconds total)