Starting phenix.real_space_refine on Mon Sep 14 00:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6shq_10203/09_2026/6shq_10203_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6shq_10203/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6shq_10203/09_2026/6shq_10203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6shq_10203/09_2026/6shq_10203.map" model { file = "/net/cci-nas-00/data/ceres_data/6shq_10203/09_2026/6shq_10203_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6shq_10203/09_2026/6shq_10203_trim.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 8.06, per 1000 atoms: 0.30 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: 2.40 Conformation dependent library (CDL) restraints added in 1.4 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: 0.66 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: 7.45 Time building geometry restraints manager: 3.31 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: 48110 3.91 - 7.82: 742 7.82 - 11.73: 51 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: 12035 24.64 - 49.29: 637 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: 1354 0.091 - 0.183: 533 0.183 - 0.274: 120 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: 0.04 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.100 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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= 0.540 Angle : 1.279 7.784 18836 Z= 0.753 Chirality : 0.104 0.456 2054 Planarity : 0.013 0.075 2462 Dihedral : 14.458 123.214 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/Z covalent geometry : bond 0.01061 / 0.54 (13878) covalent geometry : angle 1.27949 / 0.75 (18836) hydrogen bonds : bond 0.21272 / 14.54 ( 334) hydrogen bonds : angle 9.44066 / 6.56 ( 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 : 0.687 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: 0.2962 time to fit residues: 136.5274 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 : 0.660 ------------------------------------------------------------------------------- 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... 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 = 0.3683 r_free = 0.3683 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116741 restraints weight = 101498.856| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.70 r_work: 0.3133 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13878 Z= 0.136 Angle : 0.660 6.315 18836 Z= 0.337 Chirality : 0.047 0.170 2054 Planarity : 0.006 0.047 2462 Dihedral : 9.135 96.101 1995 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.93 % Allowed : 6.84 % Favored : 91.23 % 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: -2.93 (0.17), residues: 1714 helix: -2.87 (0.19), residues: 450 sheet: -1.48 (0.37), residues: 188 loop : -1.64 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 107 TYR 0.011 0.002 TYR D 114 PHE 0.015 0.002 PHE D 91 TRP 0.010 0.001 TRP A 284 HIS 0.009 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13878) covalent geometry : angle 0.65977 / 0.34 (18836) hydrogen bonds : bond 0.04484 / 2.93 ( 334) hydrogen bonds : angle 6.00928 / 4.21 ( 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 237 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.584 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 142 ASP cc_start: 0.8387 (p0) cc_final: 0.7911 (p0) REVERT: A 193 VAL cc_start: 0.8785 (p) cc_final: 0.8572 (m) REVERT: A 198 ASN cc_start: 0.8439 (t0) cc_final: 0.8238 (p0) REVERT: A 411 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8110 (mp0) REVERT: A 428 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8285 (mmmt) REVERT: D 35 ASP cc_start: 0.8617 (m-30) cc_final: 0.8199 (t0) REVERT: D 243 ASP cc_start: 0.7472 (t0) cc_final: 0.7161 (t0) REVERT: D 303 ASN cc_start: 0.8818 (m-40) cc_final: 0.8497 (m-40) REVERT: D 421 MET cc_start: 0.8920 (mtt) cc_final: 0.8638 (mtt) REVERT: C 107 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7791 (ptm-80) REVERT: C 142 ASP cc_start: 0.8164 (p0) cc_final: 0.7787 (p0) REVERT: C 234 GLU cc_start: 0.8339 (pm20) cc_final: 0.8054 (mp0) REVERT: C 289 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8088 (p0) REVERT: C 328 MET cc_start: 0.8195 (mtp) cc_final: 0.7895 (mtp) REVERT: C 428 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8258 (mmmt) REVERT: B 35 ASP cc_start: 0.8526 (m-30) cc_final: 0.8131 (t0) REVERT: B 243 ASP cc_start: 0.7436 (t0) cc_final: 0.7112 (t0) REVERT: B 303 ASN cc_start: 0.8836 (m-40) cc_final: 0.8580 (m-40) REVERT: B 375 ARG cc_start: 0.8258 (ttm110) cc_final: 0.8002 (ttm110) REVERT: B 421 MET cc_start: 0.8985 (mtt) cc_final: 0.8694 (mtt) outliers start: 20 outliers final: 8 residues processed: 226 average time/residue: 0.2938 time to fit residues: 94.0161 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 112 ASN 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 16 LEU 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: 0.9990 chunk 70 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121515 restraints weight = 103458.224| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.80 r_work: 0.3223 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13878 Z= 0.141 Angle : 0.590 6.478 18836 Z= 0.297 Chirality : 0.046 0.167 2054 Planarity : 0.005 0.047 2462 Dihedral : 8.004 92.138 1975 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.38 % Allowed : 7.94 % Favored : 90.68 % 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: -2.45 (0.18), residues: 1714 helix: -2.19 (0.22), residues: 446 sheet: -1.13 (0.38), residues: 188 loop : -1.49 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 375 TYR 0.006 0.001 TYR A 222 PHE 0.009 0.001 PHE C 218 TRP 0.008 0.001 TRP D 284 HIS 0.006 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13878) covalent geometry : angle 0.59012 / 0.30 (18836) hydrogen bonds : bond 0.03943 / 2.55 ( 334) hydrogen bonds : angle 5.27983 / 3.69 ( 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 205 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.761 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: 0.8199 (p0) cc_final: 0.7609 (p0) REVERT: A 152 MET cc_start: 0.9104 (ttp) cc_final: 0.8858 (ttp) REVERT: A 198 ASN cc_start: 0.8575 (t0) cc_final: 0.8274 (p0) REVERT: A 411 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8203 (mp0) REVERT: A 428 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8191 (mmmt) REVERT: D 35 ASP cc_start: 0.8628 (m-30) cc_final: 0.7995 (t0) REVERT: D 243 ASP cc_start: 0.7562 (t0) cc_final: 0.7226 (t0) REVERT: D 281 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 296 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 303 ASN cc_start: 0.8889 (m-40) cc_final: 0.8471 (m-40) REVERT: D 421 MET cc_start: 0.8811 (mtt) cc_final: 0.8404 (mtt) REVERT: C 107 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7852 (ptm-80) REVERT: C 142 ASP cc_start: 0.7955 (p0) cc_final: 0.7582 (p0) REVERT: C 234 GLU cc_start: 0.8331 (pm20) cc_final: 0.8056 (mp0) REVERT: C 267 ASP cc_start: 0.7807 (p0) cc_final: 0.7461 (p0) REVERT: C 289 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7925 (p0) REVERT: C 428 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8197 (mmmt) REVERT: B 35 ASP cc_start: 0.8506 (m-30) cc_final: 0.7835 (t0) REVERT: B 202 MET cc_start: 0.8129 (ttp) cc_final: 0.7888 (ttp) REVERT: B 232 ARG cc_start: 0.8865 (ptp-110) cc_final: 0.8569 (ptp90) REVERT: B 303 ASN cc_start: 0.8960 (m-40) cc_final: 0.8594 (m-40) REVERT: B 385 ASP cc_start: 0.7880 (t0) cc_final: 0.7307 (t70) REVERT: B 421 MET cc_start: 0.8967 (mtt) cc_final: 0.8549 (mtt) outliers start: 12 outliers final: 8 residues processed: 198 average time/residue: 0.2899 time to fit residues: 82.1372 Evaluate side-chains 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 112 ASN 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 289 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.2980 chunk 150 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113353 restraints weight = 106689.554| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.08 r_work: 0.3143 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 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 = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13878 Z= 0.200 Angle : 0.588 6.073 18836 Z= 0.296 Chirality : 0.047 0.163 2054 Planarity : 0.005 0.061 2462 Dihedral : 7.707 79.393 1974 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.38 % Allowed : 9.05 % Favored : 89.57 % 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: -2.23 (0.18), residues: 1714 helix: -1.82 (0.23), residues: 446 sheet: -1.12 (0.37), residues: 192 loop : -1.41 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 29 TYR 0.009 0.001 TYR C 75 PHE 0.011 0.001 PHE A 56 TRP 0.011 0.001 TRP A 372 HIS 0.005 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (13878) covalent geometry : angle 0.58803 / 0.30 (18836) hydrogen bonds : bond 0.03580 / 2.30 ( 334) hydrogen bonds : angle 4.96111 / 3.48 ( 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 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.688 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: 0.8731 (mtt180) cc_final: 0.8442 (mmt90) REVERT: A 142 ASP cc_start: 0.8233 (p0) cc_final: 0.7926 (p0) REVERT: A 198 ASN cc_start: 0.8605 (t0) cc_final: 0.8289 (p0) REVERT: A 411 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8277 (mp0) REVERT: A 428 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8220 (mmmt) REVERT: D 29 ARG cc_start: 0.8095 (ttt90) cc_final: 0.7753 (ttt-90) REVERT: D 303 ASN cc_start: 0.8920 (m-40) cc_final: 0.8485 (m-40) REVERT: D 321 ASP cc_start: 0.7996 (p0) cc_final: 0.7721 (p0) REVERT: D 385 ASP cc_start: 0.7909 (t0) cc_final: 0.7270 (t70) REVERT: D 421 MET cc_start: 0.8868 (mtt) cc_final: 0.8486 (mtt) REVERT: C 107 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7913 (ptm-80) REVERT: C 234 GLU cc_start: 0.8368 (pm20) cc_final: 0.8060 (mp0) REVERT: C 411 GLU cc_start: 0.8569 (mp0) cc_final: 0.8090 (mp0) REVERT: C 428 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8154 (mmmt) REVERT: B 202 MET cc_start: 0.7951 (ttp) cc_final: 0.7744 (ttp) REVERT: B 303 ASN cc_start: 0.9008 (m-40) cc_final: 0.8625 (m-40) REVERT: B 385 ASP cc_start: 0.7999 (t0) cc_final: 0.7422 (t70) outliers start: 12 outliers final: 9 residues processed: 179 average time/residue: 0.3013 time to fit residues: 76.7678 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain D residue 163 CYS 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 C residue 328 MET Chi-restraints excluded: chain B residue 163 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112257 restraints weight = 108089.972| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.14 r_work: 0.3125 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13878 Z= 0.189 Angle : 0.574 6.007 18836 Z= 0.286 Chirality : 0.046 0.162 2054 Planarity : 0.004 0.046 2462 Dihedral : 7.342 69.961 1970 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.52 % Allowed : 8.91 % Favored : 89.57 % 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: -2.04 (0.19), residues: 1714 helix: -1.53 (0.24), residues: 446 sheet: -1.16 (0.37), residues: 192 loop : -1.32 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 375 TYR 0.007 0.001 TYR A 75 PHE 0.010 0.001 PHE C 218 TRP 0.008 0.001 TRP B 284 HIS 0.005 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (13878) covalent geometry : angle 0.57429 / 0.29 (18836) hydrogen bonds : bond 0.03371 / 2.16 ( 334) hydrogen bonds : angle 4.75979 / 3.34 ( 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 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8318 (mtt180) REVERT: A 198 ASN cc_start: 0.8595 (t0) cc_final: 0.8288 (p0) REVERT: A 234 GLU cc_start: 0.8414 (pm20) cc_final: 0.8193 (mp0) REVERT: A 411 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8222 (mp0) REVERT: A 428 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8201 (mmmt) REVERT: D 35 ASP cc_start: 0.8622 (m-30) cc_final: 0.7933 (t0) REVERT: D 302 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8388 (mpp80) REVERT: D 303 ASN cc_start: 0.8919 (m-40) cc_final: 0.8470 (m-40) REVERT: D 321 ASP cc_start: 0.7974 (p0) cc_final: 0.7725 (p0) REVERT: D 385 ASP cc_start: 0.7942 (t0) cc_final: 0.7262 (t70) REVERT: D 421 MET cc_start: 0.8944 (mtt) cc_final: 0.8512 (mtt) REVERT: C 107 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7900 (ptm-80) REVERT: C 234 GLU cc_start: 0.8308 (pm20) cc_final: 0.8006 (mp0) REVERT: C 428 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8088 (mmmt) REVERT: B 232 ARG cc_start: 0.8857 (ptp-110) cc_final: 0.8517 (ptp90) REVERT: B 302 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8365 (mpp80) REVERT: B 303 ASN cc_start: 0.9017 (m-40) cc_final: 0.8745 (m-40) REVERT: B 385 ASP cc_start: 0.8089 (t0) cc_final: 0.7520 (t70) outliers start: 14 outliers final: 9 residues processed: 172 average time/residue: 0.3023 time to fit residues: 73.1576 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER 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 107 ARG Chi-restraints excluded: chain C residue 112 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 136 optimal weight: 0.0070 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114624 restraints weight = 108151.456| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.16 r_work: 0.3163 rms_B_bonded: 3.92 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 = 0.43 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13878 Z= 0.099 Angle : 0.531 6.132 18836 Z= 0.260 Chirality : 0.045 0.160 2054 Planarity : 0.004 0.051 2462 Dihedral : 6.955 60.918 1968 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.04 % Allowed : 9.12 % Favored : 89.85 % 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: -1.72 (0.20), residues: 1714 helix: -1.14 (0.25), residues: 446 sheet: -1.14 (0.37), residues: 192 loop : -1.13 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 29 TYR 0.006 0.001 TYR D 216 PHE 0.010 0.001 PHE A 178 TRP 0.007 0.001 TRP A 88 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13878) covalent geometry : angle 0.53082 / 0.26 (18836) hydrogen bonds : bond 0.02862 / 1.87 ( 334) hydrogen bonds : angle 4.47411 / 3.12 ( 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 181 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.713 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: 0.8596 (t0) cc_final: 0.8269 (p0) REVERT: A 234 GLU cc_start: 0.8353 (pm20) cc_final: 0.8093 (mp0) REVERT: A 411 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8238 (mp0) REVERT: A 428 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8187 (mmmt) REVERT: D 35 ASP cc_start: 0.8608 (m-30) cc_final: 0.7889 (t0) REVERT: D 303 ASN cc_start: 0.8911 (m-40) cc_final: 0.8465 (m-40) REVERT: D 321 ASP cc_start: 0.7850 (p0) cc_final: 0.7585 (p0) REVERT: D 385 ASP cc_start: 0.7883 (t0) cc_final: 0.7551 (t70) REVERT: D 421 MET cc_start: 0.8928 (mtt) cc_final: 0.8452 (mtt) REVERT: C 107 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7866 (ptm-80) REVERT: C 234 GLU cc_start: 0.8305 (pm20) cc_final: 0.7992 (mp0) REVERT: C 428 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8772 (tmtt) REVERT: B 35 ASP cc_start: 0.8516 (m-30) cc_final: 0.7799 (t0) REVERT: B 232 ARG cc_start: 0.8845 (ptp-110) cc_final: 0.8512 (ptp90) REVERT: B 303 ASN cc_start: 0.9026 (m-40) cc_final: 0.8746 (m-40) REVERT: B 385 ASP cc_start: 0.7965 (t0) cc_final: 0.7672 (t70) REVERT: B 421 MET cc_start: 0.8970 (mtt) cc_final: 0.8491 (mtt) outliers start: 9 outliers final: 6 residues processed: 175 average time/residue: 0.2987 time to fit residues: 73.6040 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113314 restraints weight = 97514.200| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.94 r_work: 0.3146 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3351 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= 0.180 Angle : 0.546 6.100 18836 Z= 0.269 Chirality : 0.046 0.152 2054 Planarity : 0.004 0.056 2462 Dihedral : 6.915 63.115 1968 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.10 % Allowed : 9.12 % Favored : 89.78 % 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: -1.69 (0.19), residues: 1714 helix: -1.12 (0.25), residues: 450 sheet: -1.14 (0.36), residues: 192 loop : -1.11 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 29 TYR 0.009 0.001 TYR C 75 PHE 0.008 0.001 PHE C 259 TRP 0.008 0.001 TRP D 284 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13878) covalent geometry : angle 0.54576 / 0.27 (18836) hydrogen bonds : bond 0.02996 / 1.97 ( 334) hydrogen bonds : angle 4.52142 / 3.16 ( 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 176 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.751 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: 0.8562 (t0) cc_final: 0.8249 (p0) REVERT: A 411 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8200 (mp0) REVERT: A 428 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8110 (mmmt) REVERT: D 35 ASP cc_start: 0.8596 (m-30) cc_final: 0.7860 (t0) REVERT: D 302 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8300 (mpp80) REVERT: D 303 ASN cc_start: 0.8924 (m-40) cc_final: 0.8614 (m-40) REVERT: D 385 ASP cc_start: 0.7987 (t0) cc_final: 0.7678 (t70) REVERT: D 421 MET cc_start: 0.8944 (mtt) cc_final: 0.8478 (mtt) REVERT: C 107 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7883 (ptm-80) REVERT: C 234 GLU cc_start: 0.8248 (pm20) cc_final: 0.7928 (mp0) REVERT: C 428 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8789 (tmtt) REVERT: B 35 ASP cc_start: 0.8544 (m-30) cc_final: 0.7821 (t0) REVERT: B 213 MET cc_start: 0.9145 (mtp) cc_final: 0.8944 (mtp) REVERT: B 232 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.8537 (ptp90) REVERT: B 303 ASN cc_start: 0.9035 (m-40) cc_final: 0.8740 (m-40) REVERT: B 328 MET cc_start: 0.7436 (mtp) cc_final: 0.7062 (mmm) REVERT: B 385 ASP cc_start: 0.8023 (t0) cc_final: 0.7723 (t70) REVERT: B 421 MET cc_start: 0.8939 (mtt) cc_final: 0.8481 (mtt) outliers start: 11 outliers final: 7 residues processed: 168 average time/residue: 0.3171 time to fit residues: 75.3546 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 107 ARG Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.0060 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: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 198 ASN B 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114744 restraints weight = 114010.787| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.26 r_work: 0.3166 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3440 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= 0.096 Angle : 0.517 6.105 18836 Z= 0.252 Chirality : 0.045 0.156 2054 Planarity : 0.004 0.059 2462 Dihedral : 6.619 59.913 1968 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.10 % Allowed : 9.25 % Favored : 89.64 % 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: -1.43 (0.20), residues: 1714 helix: -0.81 (0.26), residues: 450 sheet: -1.08 (0.36), residues: 192 loop : -0.96 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 29 TYR 0.006 0.001 TYR B 216 PHE 0.005 0.001 PHE A 56 TRP 0.006 0.001 TRP A 88 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (13878) covalent geometry : angle 0.51672 / 0.25 (18836) hydrogen bonds : bond 0.02669 / 1.76 ( 334) hydrogen bonds : angle 4.35474 / 3.04 ( 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: 12 poor density : 181 time to evaluate : 0.751 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: 0.8567 (t0) cc_final: 0.8246 (p0) REVERT: A 234 GLU cc_start: 0.8277 (pm20) cc_final: 0.7959 (mp0) REVERT: A 411 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 428 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8075 (mmmt) REVERT: D 35 ASP cc_start: 0.8591 (m-30) cc_final: 0.7859 (t0) REVERT: D 303 ASN cc_start: 0.8937 (m-40) cc_final: 0.8621 (m-40) REVERT: D 385 ASP cc_start: 0.7896 (t0) cc_final: 0.7557 (t70) REVERT: D 421 MET cc_start: 0.8957 (mtt) cc_final: 0.8428 (mtt) REVERT: D 428 LYS cc_start: 0.8579 (pmtt) cc_final: 0.7816 (ptmt) REVERT: C 107 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7855 (ptm-80) REVERT: C 234 GLU cc_start: 0.8261 (pm20) cc_final: 0.7931 (mp0) REVERT: C 428 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8757 (tmtt) REVERT: B 35 ASP cc_start: 0.8521 (m-30) cc_final: 0.7803 (t0) REVERT: B 303 ASN cc_start: 0.9028 (m-40) cc_final: 0.8731 (m-40) REVERT: B 385 ASP cc_start: 0.8003 (t0) cc_final: 0.7706 (t70) REVERT: B 421 MET cc_start: 0.8993 (mtt) cc_final: 0.8489 (mtt) outliers start: 12 outliers final: 7 residues processed: 184 average time/residue: 0.3174 time to fit residues: 82.5827 Evaluate side-chains 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain D residue 16 LEU 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 B residue 16 LEU Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115694 restraints weight = 111040.224| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.20 r_work: 0.3178 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13878 Z= 0.097 Angle : 0.511 6.173 18836 Z= 0.248 Chirality : 0.045 0.155 2054 Planarity : 0.004 0.059 2462 Dihedral : 6.344 58.093 1966 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.97 % Allowed : 9.46 % Favored : 89.57 % 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: -1.29 (0.20), residues: 1714 helix: -0.56 (0.27), residues: 450 sheet: -1.10 (0.34), residues: 200 loop : -0.91 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.005 0.001 TYR B 309 PHE 0.005 0.001 PHE C 218 TRP 0.007 0.001 TRP C 113 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13878) covalent geometry : angle 0.51131 / 0.25 (18836) hydrogen bonds : bond 0.02602 / 1.73 ( 334) hydrogen bonds : angle 4.28090 / 2.98 ( 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 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.684 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: 0.8581 (t0) cc_final: 0.8232 (p0) REVERT: A 234 GLU cc_start: 0.8250 (pm20) cc_final: 0.7922 (mp0) REVERT: A 411 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8214 (mp0) REVERT: A 428 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8078 (mmmt) REVERT: D 35 ASP cc_start: 0.8539 (m-30) cc_final: 0.7820 (t0) REVERT: D 303 ASN cc_start: 0.8938 (m-40) cc_final: 0.8612 (m-40) REVERT: D 385 ASP cc_start: 0.7856 (t0) cc_final: 0.7519 (t70) REVERT: D 421 MET cc_start: 0.9011 (mtt) cc_final: 0.8495 (mtt) REVERT: D 428 LYS cc_start: 0.8543 (pmtt) cc_final: 0.7783 (ptmt) REVERT: C 107 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7873 (ptm-80) REVERT: C 234 GLU cc_start: 0.8266 (pm20) cc_final: 0.7957 (mp0) REVERT: C 428 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8731 (tmtt) REVERT: B 35 ASP cc_start: 0.8524 (m-30) cc_final: 0.7808 (t0) REVERT: B 303 ASN cc_start: 0.9030 (m-40) cc_final: 0.8722 (m-40) REVERT: B 385 ASP cc_start: 0.7993 (t0) cc_final: 0.7697 (t70) REVERT: B 421 MET cc_start: 0.9000 (mtt) cc_final: 0.8491 (mtt) outliers start: 10 outliers final: 7 residues processed: 187 average time/residue: 0.3109 time to fit residues: 82.9766 Evaluate side-chains 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 29 optimal weight: 0.0040 chunk 66 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112886 restraints weight = 118630.053| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.29 r_work: 0.3134 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3604 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= 0.164 Angle : 0.536 6.314 18836 Z= 0.262 Chirality : 0.046 0.150 2054 Planarity : 0.004 0.061 2462 Dihedral : 6.385 61.556 1964 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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: -1.31 (0.20), residues: 1714 helix: -0.55 (0.26), residues: 446 sheet: -1.10 (0.35), residues: 200 loop : -0.94 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 29 TYR 0.008 0.001 TYR C 75 PHE 0.015 0.001 PHE A 56 TRP 0.007 0.001 TRP B 284 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (13878) covalent geometry : angle 0.53564 / 0.26 (18836) hydrogen bonds : bond 0.02820 / 1.87 ( 334) hydrogen bonds : angle 4.38009 / 3.06 ( 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 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.745 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: 0.8773 (mtt180) cc_final: 0.8245 (mtt-85) REVERT: A 198 ASN cc_start: 0.8581 (t0) cc_final: 0.8233 (p0) REVERT: A 267 ASP cc_start: 0.7903 (p0) cc_final: 0.7566 (p0) REVERT: A 328 MET cc_start: 0.8130 (mmt) cc_final: 0.7815 (mmt) REVERT: A 411 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8185 (mp0) REVERT: D 35 ASP cc_start: 0.8611 (m-30) cc_final: 0.7876 (t0) REVERT: D 198 ASN cc_start: 0.7872 (p0) cc_final: 0.7545 (p0) REVERT: D 303 ASN cc_start: 0.8934 (m-40) cc_final: 0.8604 (m-40) REVERT: D 385 ASP cc_start: 0.8024 (t0) cc_final: 0.7708 (t70) REVERT: D 421 MET cc_start: 0.8979 (mtt) cc_final: 0.8447 (mtt) REVERT: D 428 LYS cc_start: 0.8545 (pmtt) cc_final: 0.7789 (ptmt) REVERT: C 107 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7725 (ptm-80) REVERT: C 234 GLU cc_start: 0.8291 (pm20) cc_final: 0.7957 (mp0) REVERT: C 428 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8726 (tmtt) REVERT: B 35 ASP cc_start: 0.8563 (m-30) cc_final: 0.7847 (t0) REVERT: B 303 ASN cc_start: 0.9038 (m-40) cc_final: 0.8724 (m-40) REVERT: B 385 ASP cc_start: 0.8057 (t0) cc_final: 0.7743 (t70) REVERT: B 421 MET cc_start: 0.9026 (mtt) cc_final: 0.8530 (mtt) outliers start: 10 outliers final: 7 residues processed: 174 average time/residue: 0.2987 time to fit residues: 73.9869 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain D residue 230 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114496 restraints weight = 112702.343| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.21 r_work: 0.3160 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13878 Z= 0.110 Angle : 0.516 6.048 18836 Z= 0.251 Chirality : 0.045 0.154 2054 Planarity : 0.004 0.057 2462 Dihedral : 6.251 59.879 1964 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.76 % Allowed : 10.29 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1714 helix: -0.39 (0.27), residues: 442 sheet: -0.98 (0.35), residues: 200 loop : -0.85 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 29 TYR 0.005 0.001 TYR C 75 PHE 0.006 0.001 PHE A 218 TRP 0.006 0.001 TRP B 284 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13878) covalent geometry : angle 0.51611 / 0.25 (18836) hydrogen bonds : bond 0.02609 / 1.74 ( 334) hydrogen bonds : angle 4.30426 / 3.01 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5923.60 seconds wall clock time: 101 minutes 13.85 seconds (6073.85 seconds total)