Starting phenix.real_space_refine on Fri Mar 6 01:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6shq_10203/03_2026/6shq_10203.map" } resolution = 3.2 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= 0.001 sd= 0.117 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 86 5.16 5 C 8538 2.51 5 N 2438 2.21 5 O 2502 1.98 5 H 13258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26826 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 424, 6610 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 424, 6610 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 6613 Chain: "D" Number of atoms: 6692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 424, 6617 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 424, 6617 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 6609 Chain: "C" Number of atoms: 6675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 424, 6610 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 424, 6610 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 6613 Chain: "B" Number of atoms: 6692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 424, 6617 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 424, 6617 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 402} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 6609 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG A 353 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 353 " occ=0.50 residue: pdb=" N AALA D 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA D 220 " occ=0.43 residue: pdb=" N AARG D 353 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG D 353 " occ=0.50 residue: pdb=" N AARG C 353 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG C 353 " occ=0.50 residue: pdb=" N AALA B 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA B 220 " occ=0.43 residue: pdb=" N AARG B 353 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 353 " occ=0.50 Time building chain proxies: 8.22, per 1000 atoms: 0.31 Number of scatterers: 26826 At special positions: 0 Unit cell: (103.653, 112.029, 101.559, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 4 15.00 O 2502 8.00 N 2438 7.00 C 8538 6.00 H 13258 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 24.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.509A pdb=" N LYS A 34 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.627A pdb=" N ASN A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.538A pdb=" N ARG A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.661A pdb=" N ASN A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.775A pdb=" N ASP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.651A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.715A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.578A pdb=" N TYR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 4.170A pdb=" N ARG A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.579A pdb=" N LEU A 425 " --> pdb=" O MET A 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 38 removed outlier: 6.658A pdb=" N ASP D 35 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 63 removed outlier: 3.601A pdb=" N ASN D 60 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.892A pdb=" N ASN D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.654A pdb=" N ALA D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 4.250A pdb=" N ASP D 126 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.766A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 232 removed outlier: 3.965A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 3.724A pdb=" N LYS D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 removed outlier: 3.543A pdb=" N TYR D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 removed outlier: 4.235A pdb=" N ARG D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.509A pdb=" N LYS C 34 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.635A pdb=" N ASN C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.544A pdb=" N ARG C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.650A pdb=" N ASN C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.780A pdb=" N ASP C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.631A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.712A pdb=" N LYS C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 removed outlier: 3.607A pdb=" N TYR C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 removed outlier: 4.147A pdb=" N ARG C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.601A pdb=" N LEU C 425 " --> pdb=" O MET C 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 6.658A pdb=" N ASP B 35 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 37 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.601A pdb=" N ASN B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.893A pdb=" N ASN B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.654A pdb=" N ALA B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.251A pdb=" N ASP B 126 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.766A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.966A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.723A pdb=" N LYS B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.543A pdb=" N TYR B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.235A pdb=" N ARG B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 101 removed outlier: 5.155A pdb=" N ARG A 68 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 210 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A 179 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 5.155A pdb=" N ARG A 68 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA A 166 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 215 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 164 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS A 163 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N HIS A 257 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 165 " --> pdb=" O HIS A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.413A pdb=" N TRP A 372 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG A 355 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS A 317 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 333 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 349 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 366 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 383 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 408 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.127A pdb=" N ARG A 378 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A 361 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ARG A 381 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASP A 363 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL A 383 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ALA A 365 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 349 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 333 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 317 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B 355 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP B 372 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 409 removed outlier: 10.222A pdb=" N VAL A 415 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG A 381 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL A 417 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 383 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A 361 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ARG A 381 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASP A 363 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL A 383 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ALA A 365 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET A 328 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET B 328 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN B 361 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG B 378 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 101 removed outlier: 5.142A pdb=" N ARG D 68 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU D 210 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY D 179 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 101 removed outlier: 5.142A pdb=" N ARG D 68 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA D 166 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 215 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR D 164 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB1, first strand: chain 'D' and resid 389 through 390 removed outlier: 6.382A pdb=" N TRP D 372 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG D 355 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS D 317 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C 333 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 349 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN C 361 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ARG C 381 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP C 363 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL C 383 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ALA C 365 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG C 378 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 395 through 396 removed outlier: 6.150A pdb=" N ARG D 378 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN D 361 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET D 328 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET C 328 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN C 361 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ARG C 381 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP C 363 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL C 383 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ALA C 365 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N VAL C 415 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ARG C 381 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL C 417 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL C 383 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.607A pdb=" N TYR D 408 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 383 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL D 366 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 349 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 333 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 317 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 355 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP C 372 " --> pdb=" O ILE C 390 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 101 removed outlier: 5.150A pdb=" N ARG C 68 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU C 210 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 179 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 98 through 101 removed outlier: 5.150A pdb=" N ARG C 68 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA C 166 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 215 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 164 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS C 163 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS C 257 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 165 " --> pdb=" O HIS C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB7, first strand: chain 'B' and resid 98 through 101 removed outlier: 5.142A pdb=" N ARG B 68 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU B 210 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 179 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 101 removed outlier: 5.142A pdb=" N ARG B 68 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA B 166 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 215 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 164 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 47 390 hydrogen bonds defined for protein. 1020 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: 6.74 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 13216 1.01 - 1.21: 54 1.21 - 1.42: 5802 1.42 - 1.62: 7932 1.62 - 1.83: 136 Bond restraints: 27140 Sorted by residual: bond pdb=" CG LEU A 313 " pdb=" CD2 LEU A 313 " ideal model delta sigma weight residual 1.521 1.361 0.160 3.30e-02 9.18e+02 2.37e+01 bond pdb=" CG LEU C 313 " pdb=" CD2 LEU C 313 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.84e+01 bond pdb=" CA VAL C 354 " pdb=" C VAL C 354 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.13e-02 7.83e+03 1.54e+01 bond pdb=" CG LEU D 313 " pdb=" CD2 LEU D 313 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.48e+01 bond pdb=" CG LEU B 313 " pdb=" CD2 LEU B 313 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.47e+01 ... (remaining 27135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 48092 3.91 - 7.82: 752 7.82 - 11.73: 59 11.73 - 15.64: 28 15.64 - 19.55: 19 Bond angle restraints: 48950 Sorted by residual: angle pdb="HG21 ILE A 189 " pdb=" CG2 ILE A 189 " pdb="HG23 ILE A 189 " ideal model delta sigma weight residual 110.00 90.45 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb="HD11 LEU A 280 " pdb=" CD1 LEU A 280 " pdb="HD13 LEU A 280 " ideal model delta sigma weight residual 110.00 90.91 19.09 3.00e+00 1.11e-01 4.05e+01 angle pdb="HD21 LEU D 288 " pdb=" CD2 LEU D 288 " pdb="HD23 LEU D 288 " ideal model delta sigma weight residual 110.00 91.22 18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb="HD21 LEU B 288 " pdb=" CD2 LEU B 288 " pdb="HD23 LEU B 288 " ideal model delta sigma weight residual 110.00 91.22 18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb="HG22 ILE C 396 " pdb=" CG2 ILE C 396 " pdb="HG23 ILE C 396 " ideal model delta sigma weight residual 110.00 92.03 17.97 3.00e+00 1.11e-01 3.59e+01 ... (remaining 48945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.64: 12034 24.64 - 49.29: 638 49.29 - 73.93: 106 73.93 - 98.57: 18 98.57 - 123.21: 4 Dihedral angle restraints: 12800 sinusoidal: 7012 harmonic: 5788 Sorted by residual: dihedral pdb=" C5' AMP D 501 " pdb=" O5' AMP D 501 " pdb=" P AMP D 501 " pdb=" O3P AMP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 63.22 -123.21 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' AMP B 501 " pdb=" O5' AMP B 501 " pdb=" P AMP B 501 " pdb=" O3P AMP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 63.21 -123.21 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' AMP A 501 " pdb=" O5' AMP A 501 " pdb=" P AMP A 501 " pdb=" O3P AMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 -174.17 114.17 1 2.00e+01 2.50e-03 3.38e+01 ... (remaining 12797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1351 0.091 - 0.183: 534 0.183 - 0.274: 122 0.274 - 0.365: 45 0.365 - 0.456: 2 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CA GLU A 311 " pdb=" N GLU A 311 " pdb=" C GLU A 311 " pdb=" CB GLU A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA VAL C 356 " pdb=" N VAL C 356 " pdb=" C VAL C 356 " pdb=" CB VAL C 356 " both_signs ideal model delta sigma weight residual False 2.44 2.89 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CG LEU D 416 " pdb=" CB LEU D 416 " pdb=" CD1 LEU D 416 " pdb=" CD2 LEU D 416 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2051 not shown) Planarity restraints: 4092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 284 " 0.018 2.00e-02 2.50e+03 9.09e-02 3.30e+02 pdb=" CG TRP C 284 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP C 284 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 284 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP C 284 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP C 284 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP C 284 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 284 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 284 " 0.073 2.00e-02 2.50e+03 pdb=" CH2 TRP C 284 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP C 284 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 TRP C 284 " -0.257 2.00e-02 2.50e+03 pdb=" HE3 TRP C 284 " -0.039 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 284 " 0.143 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 284 " -0.167 2.00e-02 2.50e+03 pdb=" HH2 TRP C 284 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 88 " 0.064 2.00e-02 2.50e+03 7.97e-02 2.54e+02 pdb=" CG TRP A 88 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 88 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 88 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 88 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP A 88 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 88 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 88 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 88 " -0.071 2.00e-02 2.50e+03 pdb=" CH2 TRP A 88 " -0.104 2.00e-02 2.50e+03 pdb=" HD1 TRP A 88 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP A 88 " -0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP A 88 " -0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 88 " -0.023 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 88 " -0.050 2.00e-02 2.50e+03 pdb=" HH2 TRP A 88 " 0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 232 " -0.112 9.50e-02 1.11e+02 1.11e-01 2.48e+02 pdb=" NE ARG A 232 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 232 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 232 " -0.081 2.00e-02 2.50e+03 pdb=" NH2 ARG A 232 " 0.129 2.00e-02 2.50e+03 pdb="HH11 ARG A 232 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 232 " 0.130 2.00e-02 2.50e+03 pdb="HH21 ARG A 232 " 0.077 2.00e-02 2.50e+03 pdb="HH22 ARG A 232 " -0.218 2.00e-02 2.50e+03 ... (remaining 4089 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2113 2.21 - 2.80: 56116 2.80 - 3.40: 71208 3.40 - 4.00: 101363 4.00 - 4.60: 156058 Nonbonded interactions: 386858 Sorted by model distance: nonbonded pdb=" O GLU A 134 " pdb=" H ALA A 220 " model vdw 1.608 2.450 nonbonded pdb=" O GLU C 134 " pdb=" H ALA C 220 " model vdw 1.639 2.450 nonbonded pdb=" O VAL B 395 " pdb="HH22 ARG B 406 " model vdw 1.644 2.450 nonbonded pdb=" O VAL D 395 " pdb="HH22 ARG D 406 " model vdw 1.644 2.450 nonbonded pdb=" H GLY A 27 " pdb=" O ILE A 72 " model vdw 1.650 2.450 ... (remaining 386853 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 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } 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=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.011 0.160 13878 Z= 0.541 Angle : 1.304 10.589 18836 Z= 0.756 Chirality : 0.105 0.456 2054 Planarity : 0.013 0.075 2462 Dihedral : 14.478 123.214 5220 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.28 % Allowed : 2.97 % Favored : 94.75 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.16), residues: 1714 helix: -4.06 (0.14), residues: 422 sheet: -1.89 (0.36), residues: 188 loop : -1.93 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.007 ARG B 86 TYR 0.054 0.010 TYR D 255 PHE 0.055 0.010 PHE D 192 TRP 0.057 0.012 TRP C 304 HIS 0.029 0.007 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.01063 (13878) covalent geometry : angle 1.30395 (18836) hydrogen bonds : bond 0.21272 ( 334) hydrogen bonds : angle 9.44066 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8319 (mmtt) REVERT: A 50 LYS cc_start: 0.8712 (ptmt) cc_final: 0.8304 (pttp) REVERT: A 92 ASN cc_start: 0.7747 (m-40) cc_final: 0.7506 (m-40) REVERT: A 130 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7688 (mtm-85) REVERT: A 134 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6686 (tp30) REVERT: A 142 ASP cc_start: 0.7380 (p0) cc_final: 0.6772 (p0) REVERT: A 198 ASN cc_start: 0.8637 (t0) cc_final: 0.8221 (p0) REVERT: A 212 SER cc_start: 0.8121 (p) cc_final: 0.7770 (p) REVERT: A 302 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7897 (mmm-85) REVERT: A 328 MET cc_start: 0.7342 (mtp) cc_final: 0.6982 (mtp) REVERT: A 386 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.5808 (tpt170) REVERT: A 411 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8104 (mp0) REVERT: A 428 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8106 (mmmt) REVERT: D 35 ASP cc_start: 0.8368 (m-30) cc_final: 0.7347 (t0) REVERT: D 172 ILE cc_start: 0.8189 (pt) cc_final: 0.7957 (mt) REVERT: D 271 GLU cc_start: 0.8248 (pt0) cc_final: 0.7913 (mm-30) REVERT: D 303 ASN cc_start: 0.8530 (m-40) cc_final: 0.8030 (m-40) REVERT: D 321 ASP cc_start: 0.7391 (p0) cc_final: 0.7161 (p0) REVERT: D 322 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8186 (ttm170) REVERT: D 375 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6438 (ttm110) REVERT: D 421 MET cc_start: 0.8166 (mtt) cc_final: 0.7757 (mtt) REVERT: C 50 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8329 (pttp) REVERT: C 107 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7678 (ptm-80) REVERT: C 130 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7540 (mtm-85) REVERT: C 134 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6617 (tp30) REVERT: C 142 ASP cc_start: 0.7247 (p0) cc_final: 0.6691 (p0) REVERT: C 148 ASP cc_start: 0.7682 (t0) cc_final: 0.7377 (t0) REVERT: C 190 ILE cc_start: 0.8473 (mm) cc_final: 0.8144 (pt) REVERT: C 194 GLU cc_start: 0.7847 (tp30) cc_final: 0.7599 (tm-30) REVERT: C 250 GLU cc_start: 0.8413 (tt0) cc_final: 0.8007 (tp30) REVERT: C 302 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7900 (mmm-85) REVERT: C 311 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8107 (mt-10) REVERT: C 328 MET cc_start: 0.7428 (mtp) cc_final: 0.6945 (mtp) REVERT: C 411 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8381 (mp0) REVERT: B 35 ASP cc_start: 0.8488 (m-30) cc_final: 0.7281 (t0) REVERT: B 172 ILE cc_start: 0.8336 (pt) cc_final: 0.7996 (mt) REVERT: B 194 GLU cc_start: 0.8100 (tp30) cc_final: 0.7429 (tm-30) REVERT: B 271 GLU cc_start: 0.8188 (pt0) cc_final: 0.7719 (mm-30) REVERT: B 303 ASN cc_start: 0.8661 (m-40) cc_final: 0.8220 (m-40) REVERT: B 421 MET cc_start: 0.8277 (mtt) cc_final: 0.7892 (mtt) outliers start: 25 outliers final: 14 residues processed: 327 average time/residue: 0.2943 time to fit residues: 133.0564 Evaluate side-chains 223 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 216 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN D 96 ASN D 147 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN B 96 ASN B 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116873 restraints weight = 101606.875| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.71 r_work: 0.3129 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13878 Z= 0.140 Angle : 0.683 7.297 18836 Z= 0.345 Chirality : 0.048 0.172 2054 Planarity : 0.006 0.048 2462 Dihedral : 8.891 98.957 1995 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.93 % Allowed : 6.77 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.17), residues: 1714 helix: -2.93 (0.19), residues: 450 sheet: -1.51 (0.37), residues: 188 loop : -1.65 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 107 TYR 0.011 0.002 TYR D 273 PHE 0.013 0.002 PHE D 91 TRP 0.016 0.002 TRP C 284 HIS 0.010 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00313 (13878) covalent geometry : angle 0.68296 (18836) hydrogen bonds : bond 0.04989 ( 334) hydrogen bonds : angle 6.12714 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8398 (p0) cc_final: 0.7920 (p0) REVERT: A 198 ASN cc_start: 0.8444 (t0) cc_final: 0.8239 (p0) REVERT: A 289 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 411 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8104 (mp0) REVERT: A 428 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8292 (mmmt) REVERT: D 35 ASP cc_start: 0.8621 (m-30) cc_final: 0.8211 (t0) REVERT: D 303 ASN cc_start: 0.8848 (m-40) cc_final: 0.8513 (m-40) REVERT: D 321 ASP cc_start: 0.8021 (p0) cc_final: 0.7616 (p0) REVERT: D 421 MET cc_start: 0.8843 (mtt) cc_final: 0.8582 (mtt) REVERT: C 107 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7788 (ptm-80) REVERT: C 142 ASP cc_start: 0.8189 (p0) cc_final: 0.7846 (p0) REVERT: C 234 GLU cc_start: 0.8348 (pm20) cc_final: 0.8052 (mp0) REVERT: C 289 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 428 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8274 (mmmt) REVERT: B 35 ASP cc_start: 0.8476 (m-30) cc_final: 0.8096 (t0) REVERT: B 303 ASN cc_start: 0.8857 (m-40) cc_final: 0.8588 (m-40) REVERT: B 421 MET cc_start: 0.8986 (mtt) cc_final: 0.8696 (mtt) outliers start: 20 outliers final: 8 residues processed: 227 average time/residue: 0.3082 time to fit residues: 97.0813 Evaluate side-chains 189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain B residue 163 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 ASN C 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114777 restraints weight = 103171.786| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.95 r_work: 0.3162 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13878 Z= 0.224 Angle : 0.643 6.597 18836 Z= 0.323 Chirality : 0.049 0.163 2054 Planarity : 0.005 0.046 2462 Dihedral : 7.856 88.438 1977 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.59 % Allowed : 8.36 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.18), residues: 1714 helix: -2.39 (0.21), residues: 446 sheet: -1.15 (0.38), residues: 188 loop : -1.61 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.008 0.001 TYR B 222 PHE 0.014 0.002 PHE B 259 TRP 0.009 0.001 TRP B 284 HIS 0.007 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00519 (13878) covalent geometry : angle 0.64256 (18836) hydrogen bonds : bond 0.04263 ( 334) hydrogen bonds : angle 5.48224 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8294 (p0) cc_final: 0.7971 (p0) REVERT: A 152 MET cc_start: 0.9208 (ttp) cc_final: 0.8976 (ttp) REVERT: A 193 VAL cc_start: 0.8449 (p) cc_final: 0.8246 (m) REVERT: A 198 ASN cc_start: 0.8575 (t0) cc_final: 0.8273 (p0) REVERT: A 289 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8121 (p0) REVERT: A 411 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8211 (mp0) REVERT: A 428 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8208 (mmmt) REVERT: D 35 ASP cc_start: 0.8643 (m-30) cc_final: 0.7990 (t0) REVERT: D 303 ASN cc_start: 0.8917 (m-40) cc_final: 0.8505 (m-40) REVERT: D 421 MET cc_start: 0.8837 (mtt) cc_final: 0.8462 (mtt) REVERT: C 107 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7834 (ptm-80) REVERT: C 142 ASP cc_start: 0.8075 (p0) cc_final: 0.7600 (p0) REVERT: C 152 MET cc_start: 0.9270 (ttt) cc_final: 0.8965 (ttp) REVERT: C 234 GLU cc_start: 0.8325 (pm20) cc_final: 0.8037 (mp0) REVERT: C 267 ASP cc_start: 0.7828 (p0) cc_final: 0.7490 (p0) REVERT: C 428 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8206 (mmmt) REVERT: B 202 MET cc_start: 0.8174 (ttp) cc_final: 0.7927 (ttp) REVERT: B 232 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.8530 (ptp90) REVERT: B 303 ASN cc_start: 0.8988 (m-40) cc_final: 0.8621 (m-40) REVERT: B 385 ASP cc_start: 0.8011 (t0) cc_final: 0.7455 (t70) REVERT: B 421 MET cc_start: 0.8929 (mtt) cc_final: 0.8546 (mtt) outliers start: 15 outliers final: 10 residues processed: 190 average time/residue: 0.3001 time to fit residues: 79.9077 Evaluate side-chains 185 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115817 restraints weight = 106077.195| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.00 r_work: 0.3179 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13878 Z= 0.127 Angle : 0.579 6.212 18836 Z= 0.286 Chirality : 0.046 0.166 2054 Planarity : 0.004 0.044 2462 Dihedral : 7.273 81.698 1974 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.38 % Allowed : 9.19 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 1714 helix: -1.93 (0.23), residues: 446 sheet: -1.08 (0.38), residues: 188 loop : -1.42 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.006 0.001 TYR B 216 PHE 0.011 0.001 PHE D 240 TRP 0.008 0.001 TRP B 284 HIS 0.006 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00293 (13878) covalent geometry : angle 0.57863 (18836) hydrogen bonds : bond 0.03544 ( 334) hydrogen bonds : angle 4.98475 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8232 (p0) cc_final: 0.7925 (p0) REVERT: A 152 MET cc_start: 0.9156 (ttp) cc_final: 0.8930 (ttp) REVERT: A 198 ASN cc_start: 0.8579 (t0) cc_final: 0.8271 (p0) REVERT: A 289 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8027 (p0) REVERT: A 411 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 428 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8207 (mmmt) REVERT: D 35 ASP cc_start: 0.8635 (m-30) cc_final: 0.7937 (t0) REVERT: D 302 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8357 (mpp80) REVERT: D 303 ASN cc_start: 0.8884 (m-40) cc_final: 0.8475 (m-40) REVERT: D 322 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7780 (mtm-85) REVERT: D 421 MET cc_start: 0.8818 (mtt) cc_final: 0.8410 (mtt) REVERT: C 107 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (ptm-80) REVERT: C 152 MET cc_start: 0.9250 (ttt) cc_final: 0.9035 (ttp) REVERT: C 234 GLU cc_start: 0.8358 (pm20) cc_final: 0.8055 (mp0) REVERT: C 411 GLU cc_start: 0.8596 (mp0) cc_final: 0.8119 (mp0) REVERT: C 428 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8175 (mmmt) REVERT: B 202 MET cc_start: 0.7979 (ttp) cc_final: 0.7763 (ttp) REVERT: B 303 ASN cc_start: 0.8997 (m-40) cc_final: 0.8624 (m-40) REVERT: B 385 ASP cc_start: 0.7955 (t0) cc_final: 0.7390 (t70) outliers start: 12 outliers final: 9 residues processed: 188 average time/residue: 0.3126 time to fit residues: 81.5538 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113627 restraints weight = 107802.041| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.12 r_work: 0.3147 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13878 Z= 0.164 Angle : 0.574 6.121 18836 Z= 0.283 Chirality : 0.046 0.162 2054 Planarity : 0.005 0.064 2462 Dihedral : 6.853 72.727 1972 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.45 % Allowed : 9.05 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.19), residues: 1714 helix: -1.61 (0.24), residues: 446 sheet: -1.16 (0.37), residues: 192 loop : -1.32 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 29 TYR 0.007 0.001 TYR D 131 PHE 0.009 0.001 PHE A 56 TRP 0.008 0.001 TRP B 284 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00382 (13878) covalent geometry : angle 0.57392 (18836) hydrogen bonds : bond 0.03312 ( 334) hydrogen bonds : angle 4.74055 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8256 (mtt180) REVERT: A 142 ASP cc_start: 0.8240 (p0) cc_final: 0.7935 (p0) REVERT: A 198 ASN cc_start: 0.8583 (t0) cc_final: 0.8268 (p0) REVERT: A 234 GLU cc_start: 0.8444 (pm20) cc_final: 0.8234 (mp0) REVERT: A 289 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8114 (p0) REVERT: A 411 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8273 (mp0) REVERT: A 428 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8192 (mmmt) REVERT: D 35 ASP cc_start: 0.8610 (m-30) cc_final: 0.7902 (t0) REVERT: D 303 ASN cc_start: 0.8915 (m-40) cc_final: 0.8476 (m-40) REVERT: D 322 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7801 (mtm-85) REVERT: D 328 MET cc_start: 0.7868 (mmm) cc_final: 0.7294 (mmt) REVERT: D 385 ASP cc_start: 0.7869 (t0) cc_final: 0.7213 (t70) REVERT: D 421 MET cc_start: 0.8879 (mtt) cc_final: 0.8450 (mtt) REVERT: C 107 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7877 (ptm-80) REVERT: C 152 MET cc_start: 0.9268 (ttt) cc_final: 0.9049 (ttp) REVERT: C 234 GLU cc_start: 0.8333 (pm20) cc_final: 0.8011 (mp0) REVERT: C 428 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8074 (mmmt) REVERT: B 35 ASP cc_start: 0.8528 (m-30) cc_final: 0.7796 (t0) REVERT: B 232 ARG cc_start: 0.8831 (ptp-110) cc_final: 0.8493 (ptp90) REVERT: B 303 ASN cc_start: 0.9010 (m-40) cc_final: 0.8611 (m-40) REVERT: B 322 ARG cc_start: 0.8543 (ttm170) cc_final: 0.8329 (mtm-85) REVERT: B 385 ASP cc_start: 0.7964 (t0) cc_final: 0.7379 (t70) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 0.3034 time to fit residues: 74.1183 Evaluate side-chains 176 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113485 restraints weight = 108900.140| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.12 r_work: 0.3145 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13878 Z= 0.162 Angle : 0.565 6.029 18836 Z= 0.277 Chirality : 0.046 0.159 2054 Planarity : 0.004 0.073 2462 Dihedral : 6.564 61.847 1970 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.45 % Allowed : 8.84 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.19), residues: 1714 helix: -1.31 (0.25), residues: 446 sheet: -1.18 (0.37), residues: 192 loop : -1.19 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 29 TYR 0.007 0.001 TYR C 75 PHE 0.013 0.001 PHE A 178 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00377 (13878) covalent geometry : angle 0.56479 (18836) hydrogen bonds : bond 0.03157 ( 334) hydrogen bonds : angle 4.65404 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8579 (t0) cc_final: 0.8260 (p0) REVERT: A 234 GLU cc_start: 0.8364 (pm20) cc_final: 0.8037 (mp0) REVERT: A 411 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8232 (mp0) REVERT: A 428 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8192 (mmmt) REVERT: D 29 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7581 (ttt-90) REVERT: D 35 ASP cc_start: 0.8603 (m-30) cc_final: 0.7893 (t0) REVERT: D 302 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8381 (mpp80) REVERT: D 303 ASN cc_start: 0.8924 (m-40) cc_final: 0.8481 (m-40) REVERT: D 322 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.7811 (mtm-85) REVERT: D 328 MET cc_start: 0.7841 (mmm) cc_final: 0.7184 (mmt) REVERT: D 385 ASP cc_start: 0.7937 (t0) cc_final: 0.7657 (t70) REVERT: D 421 MET cc_start: 0.8930 (mtt) cc_final: 0.8458 (mtt) REVERT: C 107 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7825 (ptm-80) REVERT: C 234 GLU cc_start: 0.8265 (pm20) cc_final: 0.7940 (mp0) REVERT: C 428 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8054 (mmmt) REVERT: B 35 ASP cc_start: 0.8523 (m-30) cc_final: 0.7797 (t0) REVERT: B 303 ASN cc_start: 0.9014 (m-40) cc_final: 0.8725 (m-40) REVERT: B 385 ASP cc_start: 0.8038 (t0) cc_final: 0.7388 (t70) outliers start: 14 outliers final: 10 residues processed: 179 average time/residue: 0.3206 time to fit residues: 79.8018 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114007 restraints weight = 97301.908| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.94 r_work: 0.3155 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13878 Z= 0.149 Angle : 0.552 6.087 18836 Z= 0.269 Chirality : 0.046 0.155 2054 Planarity : 0.004 0.055 2462 Dihedral : 6.290 58.258 1968 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.45 % Allowed : 9.19 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.19), residues: 1714 helix: -1.13 (0.25), residues: 446 sheet: -1.15 (0.37), residues: 192 loop : -1.15 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.007 0.001 TYR C 75 PHE 0.007 0.001 PHE A 218 TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00348 (13878) covalent geometry : angle 0.55222 (18836) hydrogen bonds : bond 0.02967 ( 334) hydrogen bonds : angle 4.52761 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8564 (t0) cc_final: 0.8246 (p0) REVERT: A 234 GLU cc_start: 0.8327 (pm20) cc_final: 0.8010 (mp0) REVERT: A 411 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8215 (mp0) REVERT: A 428 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8103 (mmmt) REVERT: D 35 ASP cc_start: 0.8584 (m-30) cc_final: 0.7983 (t0) REVERT: D 302 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8285 (mpp80) REVERT: D 303 ASN cc_start: 0.8933 (m-40) cc_final: 0.8467 (m-40) REVERT: D 328 MET cc_start: 0.7829 (mmm) cc_final: 0.7152 (mmt) REVERT: D 385 ASP cc_start: 0.7985 (t0) cc_final: 0.7665 (t70) REVERT: D 421 MET cc_start: 0.8942 (mtt) cc_final: 0.8463 (mtt) REVERT: C 107 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7890 (ptm-80) REVERT: C 234 GLU cc_start: 0.8238 (pm20) cc_final: 0.7913 (mp0) REVERT: C 428 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8778 (tmtt) REVERT: B 35 ASP cc_start: 0.8514 (m-30) cc_final: 0.7902 (t0) REVERT: B 302 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8311 (mpp80) REVERT: B 303 ASN cc_start: 0.9016 (m-40) cc_final: 0.8722 (m-40) REVERT: B 322 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8274 (ttm170) REVERT: B 385 ASP cc_start: 0.7987 (t0) cc_final: 0.7662 (t70) REVERT: B 421 MET cc_start: 0.8932 (mtt) cc_final: 0.8475 (mtt) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 0.3112 time to fit residues: 74.7306 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 156 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114417 restraints weight = 114291.173| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.23 r_work: 0.3163 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13878 Z= 0.109 Angle : 0.535 6.111 18836 Z= 0.258 Chirality : 0.045 0.157 2054 Planarity : 0.004 0.060 2462 Dihedral : 6.041 52.906 1968 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.24 % Allowed : 9.25 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1714 helix: -0.90 (0.26), residues: 450 sheet: -1.12 (0.36), residues: 192 loop : -1.00 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.005 0.001 TYR C 75 PHE 0.007 0.001 PHE A 178 TRP 0.007 0.001 TRP A 88 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00254 (13878) covalent geometry : angle 0.53467 (18836) hydrogen bonds : bond 0.02726 ( 334) hydrogen bonds : angle 4.41251 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8563 (t0) cc_final: 0.8243 (p0) REVERT: A 411 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8248 (mp0) REVERT: A 428 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8088 (mmmt) REVERT: D 35 ASP cc_start: 0.8539 (m-30) cc_final: 0.7842 (t0) REVERT: D 302 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8316 (mpp80) REVERT: D 303 ASN cc_start: 0.8937 (m-40) cc_final: 0.8477 (m-40) REVERT: D 322 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7923 (mtm-85) REVERT: D 328 MET cc_start: 0.7816 (mmm) cc_final: 0.7132 (mmt) REVERT: D 385 ASP cc_start: 0.7912 (t0) cc_final: 0.7590 (t70) REVERT: D 421 MET cc_start: 0.8955 (mtt) cc_final: 0.8448 (mtt) REVERT: D 428 LYS cc_start: 0.8578 (pmtt) cc_final: 0.7816 (ptmt) REVERT: C 107 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7726 (ptm-80) REVERT: C 234 GLU cc_start: 0.8235 (pm20) cc_final: 0.7934 (mp0) REVERT: C 428 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8779 (tmtt) REVERT: B 35 ASP cc_start: 0.8521 (m-30) cc_final: 0.7819 (t0) REVERT: B 303 ASN cc_start: 0.9021 (m-40) cc_final: 0.8723 (m-40) REVERT: B 328 MET cc_start: 0.7841 (mmm) cc_final: 0.7045 (mmt) REVERT: B 385 ASP cc_start: 0.8010 (t0) cc_final: 0.7711 (t70) REVERT: B 421 MET cc_start: 0.8984 (mtt) cc_final: 0.8482 (mtt) outliers start: 13 outliers final: 8 residues processed: 184 average time/residue: 0.3144 time to fit residues: 79.9136 Evaluate side-chains 182 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112599 restraints weight = 112118.150| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.17 r_work: 0.3138 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13878 Z= 0.164 Angle : 0.551 6.117 18836 Z= 0.268 Chirality : 0.046 0.152 2054 Planarity : 0.004 0.061 2462 Dihedral : 5.935 55.444 1966 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1714 helix: -0.85 (0.26), residues: 446 sheet: -1.24 (0.35), residues: 200 loop : -1.03 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 375 TYR 0.008 0.001 TYR C 75 PHE 0.007 0.001 PHE C 218 TRP 0.007 0.001 TRP B 284 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00383 (13878) covalent geometry : angle 0.55119 (18836) hydrogen bonds : bond 0.02890 ( 334) hydrogen bonds : angle 4.48465 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8600 (t0) cc_final: 0.8240 (p0) REVERT: A 234 GLU cc_start: 0.8276 (pm20) cc_final: 0.7944 (mp0) REVERT: A 411 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8196 (mp0) REVERT: D 35 ASP cc_start: 0.8584 (m-30) cc_final: 0.7958 (t0) REVERT: D 302 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8312 (mpp80) REVERT: D 303 ASN cc_start: 0.8940 (m-40) cc_final: 0.8613 (m-40) REVERT: D 328 MET cc_start: 0.7857 (mmm) cc_final: 0.7168 (mmt) REVERT: D 385 ASP cc_start: 0.8003 (t0) cc_final: 0.7682 (t70) REVERT: D 421 MET cc_start: 0.8959 (mtt) cc_final: 0.8468 (mtt) REVERT: D 428 LYS cc_start: 0.8552 (pmtt) cc_final: 0.7788 (ptmt) REVERT: C 107 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7945 (ptm-80) REVERT: C 234 GLU cc_start: 0.8261 (pm20) cc_final: 0.7936 (mp0) REVERT: C 428 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8785 (tmtt) REVERT: B 35 ASP cc_start: 0.8463 (m-30) cc_final: 0.7858 (t0) REVERT: B 302 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8308 (mpp80) REVERT: B 303 ASN cc_start: 0.9023 (m-40) cc_final: 0.8711 (m-40) REVERT: B 385 ASP cc_start: 0.8029 (t0) cc_final: 0.7713 (t70) REVERT: B 421 MET cc_start: 0.8964 (mtt) cc_final: 0.8469 (mtt) outliers start: 13 outliers final: 8 residues processed: 177 average time/residue: 0.3096 time to fit residues: 76.1165 Evaluate side-chains 179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 388 CYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114307 restraints weight = 117944.649| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.27 r_work: 0.3158 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13878 Z= 0.103 Angle : 0.532 6.124 18836 Z= 0.256 Chirality : 0.045 0.154 2054 Planarity : 0.004 0.058 2462 Dihedral : 5.753 52.416 1964 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.97 % Allowed : 9.88 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.20), residues: 1714 helix: -0.65 (0.27), residues: 442 sheet: -1.13 (0.35), residues: 200 loop : -0.90 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.005 0.001 TYR C 75 PHE 0.006 0.001 PHE A 178 TRP 0.006 0.001 TRP A 284 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00240 (13878) covalent geometry : angle 0.53186 (18836) hydrogen bonds : bond 0.02674 ( 334) hydrogen bonds : angle 4.37044 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8597 (t0) cc_final: 0.8240 (p0) REVERT: A 234 GLU cc_start: 0.8296 (pm20) cc_final: 0.7952 (mp0) REVERT: A 411 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8206 (mp0) REVERT: D 35 ASP cc_start: 0.8545 (m-30) cc_final: 0.7839 (t0) REVERT: D 303 ASN cc_start: 0.8941 (m-40) cc_final: 0.8616 (m-40) REVERT: D 328 MET cc_start: 0.7800 (mmm) cc_final: 0.7108 (mmt) REVERT: D 385 ASP cc_start: 0.7947 (t0) cc_final: 0.7638 (t70) REVERT: D 421 MET cc_start: 0.9004 (mtt) cc_final: 0.8472 (mtt) REVERT: D 428 LYS cc_start: 0.8549 (pmtt) cc_final: 0.7786 (ptmt) REVERT: C 107 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7770 (ptm-80) REVERT: C 234 GLU cc_start: 0.8273 (pm20) cc_final: 0.7960 (mp0) REVERT: C 428 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8736 (tmtt) REVERT: B 35 ASP cc_start: 0.8468 (m-30) cc_final: 0.7774 (t0) REVERT: B 303 ASN cc_start: 0.9020 (m-40) cc_final: 0.8708 (m-40) REVERT: B 385 ASP cc_start: 0.7984 (t0) cc_final: 0.7673 (t70) REVERT: B 421 MET cc_start: 0.8997 (mtt) cc_final: 0.8482 (mtt) outliers start: 10 outliers final: 8 residues processed: 185 average time/residue: 0.3088 time to fit residues: 79.4076 Evaluate side-chains 186 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 388 CYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 388 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116165 restraints weight = 112021.345| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.20 r_work: 0.3186 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13878 Z= 0.088 Angle : 0.524 6.117 18836 Z= 0.250 Chirality : 0.045 0.152 2054 Planarity : 0.004 0.060 2462 Dihedral : 5.538 49.947 1964 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.97 % Allowed : 10.22 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1714 helix: -0.43 (0.27), residues: 442 sheet: -0.94 (0.35), residues: 200 loop : -0.84 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 375 TYR 0.005 0.001 TYR D 309 PHE 0.005 0.001 PHE A 178 TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00205 (13878) covalent geometry : angle 0.52364 (18836) hydrogen bonds : bond 0.02479 ( 334) hydrogen bonds : angle 4.23842 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5772.53 seconds wall clock time: 98 minutes 27.38 seconds (5907.38 seconds total)