Starting phenix.real_space_refine on Sat Mar 7 10:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfd_25870/03_2026/7tfd_25870.cif" } resolution = 3.16 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= 0.032 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: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 228 5.16 5 C 26386 2.51 5 N 7104 2.21 5 O 7666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41408 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "L" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3445 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "Q" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "S" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "T" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "W" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "X" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU B 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 248 " occ=0.97 residue: pdb=" N LEU E 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 248 " occ=0.97 residue: pdb=" N LEU F 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 248 " occ=0.97 residue: pdb=" N LEU J 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 248 " occ=0.97 residue: pdb=" N LEU K 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 248 " occ=0.97 residue: pdb=" N LEU L 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 248 " occ=0.97 residue: pdb=" N LEU Q 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU Q 248 " occ=0.97 residue: pdb=" N LEU R 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 248 " occ=0.97 residue: pdb=" N LEU S 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 248 " occ=0.97 residue: pdb=" N LEU T 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 248 " occ=0.97 residue: pdb=" N LEU W 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU W 248 " occ=0.97 residue: pdb=" N LEU X 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU X 248 " occ=0.97 Time building chain proxies: 9.33, per 1000 atoms: 0.23 Number of scatterers: 41408 At special positions: 0 Unit cell: (159.28, 150.48, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 228 16.00 Mg 24 11.99 O 7666 8.00 N 7104 7.00 C 26386 6.00 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9960 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 28 sheets defined 44.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 53 through 61 removed outlier: 6.580A pdb=" N TYR B 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.637A pdb=" N GLU B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 279 through 288 removed outlier: 4.517A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.599A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.701A pdb=" N THR B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.505A pdb=" N TYR B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 removed outlier: 3.639A pdb=" N ARG B 435 " --> pdb=" O HIS B 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 53 through 61 removed outlier: 6.622A pdb=" N TYR E 59 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 202 through 223 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 279 through 288 removed outlier: 4.355A pdb=" N ALA E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.556A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.575A pdb=" N THR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 Processing helix chain 'E' and resid 374 through 381 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 402 through 408 Processing helix chain 'E' and resid 408 through 428 removed outlier: 3.537A pdb=" N TYR E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 removed outlier: 3.623A pdb=" N ARG E 435 " --> pdb=" O HIS E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 53 through 61 removed outlier: 6.553A pdb=" N TYR F 59 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 61 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Processing helix chain 'F' and resid 165 through 178 removed outlier: 3.797A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 223 Processing helix chain 'F' and resid 266 through 279 Processing helix chain 'F' and resid 279 through 288 removed outlier: 4.357A pdb=" N ALA F 285 " --> pdb=" O ARG F 281 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 3.550A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.618A pdb=" N THR F 328 " --> pdb=" O GLY F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 374 through 381 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 408 through 428 removed outlier: 3.504A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR F 414 " --> pdb=" O HIS F 410 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 438 removed outlier: 3.619A pdb=" N ARG F 435 " --> pdb=" O HIS F 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 53 through 61 removed outlier: 6.564A pdb=" N TYR J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 76 Processing helix chain 'J' and resid 105 through 119 Processing helix chain 'J' and resid 165 through 178 Processing helix chain 'J' and resid 201 through 223 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 279 through 288 removed outlier: 4.404A pdb=" N ALA J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.530A pdb=" N ARG J 296 " --> pdb=" O ASN J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.546A pdb=" N THR J 328 " --> pdb=" O GLY J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 359 Processing helix chain 'J' and resid 374 through 381 Processing helix chain 'J' and resid 389 through 400 Processing helix chain 'J' and resid 402 through 408 Processing helix chain 'J' and resid 408 through 428 removed outlier: 3.507A pdb=" N TYR J 414 " --> pdb=" O HIS J 410 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 428 " --> pdb=" O ASP J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 438 removed outlier: 3.633A pdb=" N ARG J 435 " --> pdb=" O HIS J 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 53 through 61 removed outlier: 6.617A pdb=" N TYR K 59 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG K 61 " --> pdb=" O GLY K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 76 Processing helix chain 'K' and resid 105 through 119 Processing helix chain 'K' and resid 165 through 177 Processing helix chain 'K' and resid 202 through 223 Processing helix chain 'K' and resid 266 through 279 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.388A pdb=" N ALA K 285 " --> pdb=" O ARG K 281 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE K 286 " --> pdb=" O ALA K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.583A pdb=" N ARG K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 328 Processing helix chain 'K' and resid 340 through 359 Processing helix chain 'K' and resid 374 through 381 Processing helix chain 'K' and resid 389 through 400 Processing helix chain 'K' and resid 402 through 408 Processing helix chain 'K' and resid 408 through 428 removed outlier: 3.535A pdb=" N TYR K 414 " --> pdb=" O HIS K 410 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR K 428 " --> pdb=" O ASP K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 438 removed outlier: 3.604A pdb=" N ARG K 435 " --> pdb=" O HIS K 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 53 through 61 removed outlier: 6.590A pdb=" N TYR L 59 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL L 60 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 76 Processing helix chain 'L' and resid 105 through 119 Processing helix chain 'L' and resid 165 through 178 removed outlier: 3.714A pdb=" N GLU L 169 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 223 Processing helix chain 'L' and resid 266 through 279 Processing helix chain 'L' and resid 279 through 288 removed outlier: 4.371A pdb=" N ALA L 285 " --> pdb=" O ARG L 281 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.585A pdb=" N ARG L 296 " --> pdb=" O ASN L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 328 removed outlier: 3.771A pdb=" N THR L 328 " --> pdb=" O GLY L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 359 Processing helix chain 'L' and resid 374 through 381 Processing helix chain 'L' and resid 389 through 400 Processing helix chain 'L' and resid 402 through 408 Processing helix chain 'L' and resid 408 through 428 removed outlier: 3.531A pdb=" N TYR L 414 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR L 428 " --> pdb=" O ASP L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 438 removed outlier: 3.654A pdb=" N ARG L 435 " --> pdb=" O HIS L 431 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'Q' and resid 53 through 61 removed outlier: 6.585A pdb=" N TYR Q 59 " --> pdb=" O ILE Q 56 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 76 Processing helix chain 'Q' and resid 105 through 119 Processing helix chain 'Q' and resid 165 through 178 Processing helix chain 'Q' and resid 201 through 223 Processing helix chain 'Q' and resid 266 through 279 Processing helix chain 'Q' and resid 279 through 288 removed outlier: 4.370A pdb=" N ALA Q 285 " --> pdb=" O ARG Q 281 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 297 removed outlier: 3.572A pdb=" N ARG Q 296 " --> pdb=" O ASN Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 328 removed outlier: 3.636A pdb=" N THR Q 328 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 359 Processing helix chain 'Q' and resid 374 through 381 Processing helix chain 'Q' and resid 389 through 400 Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 408 through 428 removed outlier: 3.512A pdb=" N TYR Q 414 " --> pdb=" O HIS Q 410 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 438 removed outlier: 3.611A pdb=" N ARG Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 40 through 46 Processing helix chain 'R' and resid 53 through 61 removed outlier: 6.621A pdb=" N TYR R 59 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 60 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 76 Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 165 through 178 Processing helix chain 'R' and resid 202 through 223 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.390A pdb=" N ALA R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.573A pdb=" N ARG R 296 " --> pdb=" O ASN R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 328 removed outlier: 3.622A pdb=" N THR R 328 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 359 Processing helix chain 'R' and resid 374 through 381 Processing helix chain 'R' and resid 389 through 400 Processing helix chain 'R' and resid 402 through 408 Processing helix chain 'R' and resid 408 through 428 removed outlier: 3.526A pdb=" N TYR R 414 " --> pdb=" O HIS R 410 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR R 428 " --> pdb=" O ASP R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 438 removed outlier: 3.624A pdb=" N ARG R 435 " --> pdb=" O HIS R 431 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 16 Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 53 through 61 removed outlier: 6.575A pdb=" N TYR S 59 " --> pdb=" O ILE S 56 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 76 Processing helix chain 'S' and resid 105 through 119 Processing helix chain 'S' and resid 165 through 178 Processing helix chain 'S' and resid 202 through 223 Processing helix chain 'S' and resid 266 through 279 Processing helix chain 'S' and resid 279 through 288 removed outlier: 4.450A pdb=" N ALA S 285 " --> pdb=" O ARG S 281 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 297 removed outlier: 3.566A pdb=" N ARG S 296 " --> pdb=" O ASN S 292 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU S 297 " --> pdb=" O SER S 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 292 through 297' Processing helix chain 'S' and resid 324 through 328 removed outlier: 3.623A pdb=" N THR S 328 " --> pdb=" O GLY S 325 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 359 Processing helix chain 'S' and resid 374 through 381 Processing helix chain 'S' and resid 389 through 400 Processing helix chain 'S' and resid 402 through 408 Processing helix chain 'S' and resid 408 through 428 removed outlier: 3.529A pdb=" N TYR S 414 " --> pdb=" O HIS S 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR S 428 " --> pdb=" O ASP S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 431 through 438 removed outlier: 3.647A pdb=" N ARG S 435 " --> pdb=" O HIS S 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 53 through 61 removed outlier: 6.557A pdb=" N TYR T 59 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL T 60 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG T 61 " --> pdb=" O GLY T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 76 Processing helix chain 'T' and resid 105 through 119 Processing helix chain 'T' and resid 165 through 178 removed outlier: 3.883A pdb=" N GLU T 169 " --> pdb=" O ASN T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 223 Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.502A pdb=" N HIS T 279 " --> pdb=" O GLY T 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 288 removed outlier: 4.324A pdb=" N ALA T 285 " --> pdb=" O ARG T 281 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 297 removed outlier: 3.594A pdb=" N ARG T 296 " --> pdb=" O ASN T 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 328 removed outlier: 3.742A pdb=" N THR T 328 " --> pdb=" O GLY T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 359 Processing helix chain 'T' and resid 374 through 381 Processing helix chain 'T' and resid 389 through 400 Processing helix chain 'T' and resid 402 through 408 Processing helix chain 'T' and resid 408 through 428 removed outlier: 3.502A pdb=" N ALA T 413 " --> pdb=" O ASP T 409 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR T 414 " --> pdb=" O HIS T 410 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR T 428 " --> pdb=" O ASP T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 438 removed outlier: 3.629A pdb=" N ARG T 435 " --> pdb=" O HIS T 431 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 15 Processing helix chain 'W' and resid 40 through 46 Processing helix chain 'W' and resid 53 through 61 removed outlier: 6.554A pdb=" N TYR W 59 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL W 60 " --> pdb=" O GLU W 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG W 61 " --> pdb=" O GLY W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 76 Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 165 through 178 removed outlier: 3.807A pdb=" N GLU W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 223 Processing helix chain 'W' and resid 266 through 279 Processing helix chain 'W' and resid 279 through 288 removed outlier: 4.441A pdb=" N ALA W 285 " --> pdb=" O ARG W 281 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 3.593A pdb=" N ARG W 296 " --> pdb=" O ASN W 292 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 292 through 297' Processing helix chain 'W' and resid 324 through 328 Processing helix chain 'W' and resid 340 through 359 Processing helix chain 'W' and resid 374 through 381 Processing helix chain 'W' and resid 389 through 400 Processing helix chain 'W' and resid 402 through 408 Processing helix chain 'W' and resid 408 through 428 removed outlier: 3.516A pdb=" N TYR W 414 " --> pdb=" O HIS W 410 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR W 428 " --> pdb=" O ASP W 424 " (cutoff:3.500A) Processing helix chain 'W' and resid 431 through 438 removed outlier: 3.630A pdb=" N ARG W 435 " --> pdb=" O HIS W 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 53 through 61 removed outlier: 6.614A pdb=" N TYR X 59 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL X 60 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG X 61 " --> pdb=" O GLY X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 76 Processing helix chain 'X' and resid 105 through 119 Processing helix chain 'X' and resid 165 through 177 removed outlier: 3.842A pdb=" N GLU X 169 " --> pdb=" O ASN X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 223 Processing helix chain 'X' and resid 266 through 279 Processing helix chain 'X' and resid 279 through 288 removed outlier: 4.375A pdb=" N ALA X 285 " --> pdb=" O ARG X 281 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE X 286 " --> pdb=" O ALA X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 297 removed outlier: 3.568A pdb=" N ARG X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 328 Processing helix chain 'X' and resid 340 through 359 Processing helix chain 'X' and resid 374 through 381 Processing helix chain 'X' and resid 389 through 400 Processing helix chain 'X' and resid 402 through 408 Processing helix chain 'X' and resid 408 through 428 removed outlier: 3.533A pdb=" N TYR X 414 " --> pdb=" O HIS X 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR X 428 " --> pdb=" O ASP X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 438 removed outlier: 3.621A pdb=" N ARG X 435 " --> pdb=" O HIS X 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 37 current: chain 'B' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 67 through 71 current: chain 'B' and resid 86 through 95 Processing sheet with id=AA2, first strand: chain 'B' and resid 124 through 138 removed outlier: 7.509A pdb=" N LEU B 135 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 137 " --> pdb=" O THR B 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 148 current: chain 'B' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 192 through 197 current: chain 'B' and resid 318 through 319 Processing sheet with id=AA3, first strand: chain 'E' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 31 through 37 current: chain 'E' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 67 through 71 current: chain 'E' and resid 86 through 95 Processing sheet with id=AA4, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'E' and resid 132 through 138 removed outlier: 7.523A pdb=" N LEU E 135 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU E 147 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS E 137 " --> pdb=" O THR E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 148 current: chain 'E' and resid 192 through 197 Processing sheet with id=AA6, first strand: chain 'F' and resid 31 through 37 removed outlier: 4.955A pdb=" N VAL F 17 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA F 88 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE F 19 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 90 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG F 21 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS F 92 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN F 23 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 94 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N THR F 25 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE F 91 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR F 75 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N ASP F 93 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N LEU F 73 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N TYR F 95 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 200 through 201 removed outlier: 4.034A pdb=" N HIS F 243 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 132 through 138 removed outlier: 7.605A pdb=" N LEU F 135 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU F 147 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS F 137 " --> pdb=" O THR F 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 144 through 148 current: chain 'F' and resid 192 through 197 Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 31 through 37 current: chain 'J' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 67 through 71 current: chain 'J' and resid 86 through 95 Processing sheet with id=AB1, first strand: chain 'J' and resid 124 through 138 removed outlier: 7.537A pdb=" N LEU J 135 " --> pdb=" O GLU J 147 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU J 147 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS J 137 " --> pdb=" O THR J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 144 through 148 current: chain 'J' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 192 through 197 current: chain 'J' and resid 318 through 319 Processing sheet with id=AB2, first strand: chain 'K' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 31 through 37 current: chain 'K' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 67 through 71 current: chain 'K' and resid 86 through 95 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 138 removed outlier: 5.189A pdb=" N GLU K 147 " --> pdb=" O LYS K 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 144 through 148 current: chain 'K' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 192 through 197 current: chain 'K' and resid 318 through 319 Processing sheet with id=AB4, first strand: chain 'L' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 31 through 37 current: chain 'L' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 71 current: chain 'L' and resid 86 through 95 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 138 removed outlier: 5.128A pdb=" N GLU L 147 " --> pdb=" O LYS L 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 144 through 148 current: chain 'L' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 192 through 197 current: chain 'L' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'Q' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 31 through 37 current: chain 'Q' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 67 through 71 current: chain 'Q' and resid 86 through 95 Processing sheet with id=AB7, first strand: chain 'Q' and resid 124 through 138 removed outlier: 5.125A pdb=" N GLU Q 147 " --> pdb=" O LYS Q 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 144 through 148 current: chain 'Q' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 192 through 197 current: chain 'Q' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'R' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 31 through 37 current: chain 'R' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 67 through 71 current: chain 'R' and resid 86 through 95 Processing sheet with id=AB9, first strand: chain 'R' and resid 124 through 138 removed outlier: 5.026A pdb=" N GLU R 147 " --> pdb=" O LYS R 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 144 through 148 current: chain 'R' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 192 through 197 current: chain 'R' and resid 253 through 254 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 253 through 254 current: chain 'R' and resid 318 through 319 Processing sheet with id=AC1, first strand: chain 'S' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 31 through 37 current: chain 'S' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 67 through 71 current: chain 'S' and resid 86 through 95 Processing sheet with id=AC2, first strand: chain 'S' and resid 124 through 138 removed outlier: 7.464A pdb=" N LEU S 135 " --> pdb=" O GLU S 147 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU S 147 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS S 137 " --> pdb=" O THR S 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 144 through 148 current: chain 'S' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 192 through 197 current: chain 'S' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'T' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 31 through 37 current: chain 'T' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 67 through 71 current: chain 'T' and resid 86 through 95 Processing sheet with id=AC4, first strand: chain 'T' and resid 200 through 201 Processing sheet with id=AC5, first strand: chain 'T' and resid 132 through 138 removed outlier: 5.395A pdb=" N GLU T 147 " --> pdb=" O LYS T 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 144 through 148 current: chain 'T' and resid 192 through 197 Processing sheet with id=AC6, first strand: chain 'W' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 31 through 37 current: chain 'W' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 67 through 71 current: chain 'W' and resid 86 through 95 Processing sheet with id=AC7, first strand: chain 'W' and resid 124 through 138 removed outlier: 7.504A pdb=" N LEU W 135 " --> pdb=" O GLU W 147 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU W 147 " --> pdb=" O LEU W 135 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS W 137 " --> pdb=" O THR W 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 144 through 148 current: chain 'W' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 192 through 197 current: chain 'W' and resid 318 through 319 Processing sheet with id=AC8, first strand: chain 'X' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 31 through 37 current: chain 'X' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 67 through 71 current: chain 'X' and resid 86 through 95 Processing sheet with id=AC9, first strand: chain 'X' and resid 200 through 201 Processing sheet with id=AD1, first strand: chain 'X' and resid 132 through 138 removed outlier: 7.536A pdb=" N LEU X 135 " --> pdb=" O GLU X 147 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU X 147 " --> pdb=" O LEU X 135 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS X 137 " --> pdb=" O THR X 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 144 through 148 current: chain 'X' and resid 192 through 197 1594 hydrogen bonds defined for protein. 4548 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: 8.68 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10766 1.33 - 1.45: 7714 1.45 - 1.57: 23468 1.57 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 42356 Sorted by residual: bond pdb=" N ASN S 334 " pdb=" CA ASN S 334 " ideal model delta sigma weight residual 1.461 1.494 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" C ALA S 303 " pdb=" N PRO S 304 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.01e-02 9.80e+03 1.10e+01 bond pdb=" N ILE T 370 " pdb=" CA ILE T 370 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.31e+00 bond pdb=" N ASP S 336 " pdb=" CA ASP S 336 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N VAL S 332 " pdb=" CA VAL S 332 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.49e+00 ... (remaining 42351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 56114 2.03 - 4.06: 1275 4.06 - 6.10: 100 6.10 - 8.13: 31 8.13 - 10.16: 3 Bond angle restraints: 57523 Sorted by residual: angle pdb=" C GLY S 142 " pdb=" N ASP S 143 " pdb=" CA ASP S 143 " ideal model delta sigma weight residual 121.83 127.99 -6.16 1.56e+00 4.11e-01 1.56e+01 angle pdb=" N VAL W 307 " pdb=" CA VAL W 307 " pdb=" C VAL W 307 " ideal model delta sigma weight residual 106.32 112.57 -6.25 1.61e+00 3.86e-01 1.51e+01 angle pdb=" N GLY R 178 " pdb=" CA GLY R 178 " pdb=" C GLY R 178 " ideal model delta sigma weight residual 115.27 109.98 5.29 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C ASN K 334 " pdb=" CA ASN K 334 " pdb=" CB ASN K 334 " ideal model delta sigma weight residual 112.76 105.89 6.87 1.86e+00 2.89e-01 1.36e+01 angle pdb=" CA MET E 242 " pdb=" C MET E 242 " pdb=" O MET E 242 " ideal model delta sigma weight residual 121.89 117.35 4.54 1.29e+00 6.01e-01 1.24e+01 ... (remaining 57518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 23276 17.98 - 35.96: 1817 35.96 - 53.94: 384 53.94 - 71.92: 65 71.92 - 89.90: 39 Dihedral angle restraints: 25581 sinusoidal: 10101 harmonic: 15480 Sorted by residual: dihedral pdb=" CA ILE R 370 " pdb=" C ILE R 370 " pdb=" N TYR R 371 " pdb=" CA TYR R 371 " ideal model delta harmonic sigma weight residual 180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU E 22 " pdb=" C LEU E 22 " pdb=" N GLN E 23 " pdb=" CA GLN E 23 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ILE F 370 " pdb=" C ILE F 370 " pdb=" N TYR F 371 " pdb=" CA TYR F 371 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 25578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4644 0.043 - 0.086: 1235 0.086 - 0.129: 387 0.129 - 0.172: 38 0.172 - 0.215: 8 Chirality restraints: 6312 Sorted by residual: chirality pdb=" CG LEU Q 157 " pdb=" CB LEU Q 157 " pdb=" CD1 LEU Q 157 " pdb=" CD2 LEU Q 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE S 370 " pdb=" CA ILE S 370 " pdb=" CG1 ILE S 370 " pdb=" CG2 ILE S 370 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL T 372 " pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CB VAL T 372 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 6309 not shown) Planarity restraints: 7523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN S 369 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ASN S 369 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN S 369 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE S 370 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 336 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ASP T 336 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP T 336 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO T 337 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 242 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C MET Q 242 " -0.034 2.00e-02 2.50e+03 pdb=" O MET Q 242 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS Q 243 " 0.011 2.00e-02 2.50e+03 ... (remaining 7520 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 497 2.60 - 3.17: 36993 3.17 - 3.75: 67352 3.75 - 4.32: 91948 4.32 - 4.90: 153501 Nonbonded interactions: 350291 Sorted by model distance: nonbonded pdb=" OE2 GLU T 331 " pdb="MG MG T 502 " model vdw 2.024 2.170 nonbonded pdb=" OE2 GLU T 132 " pdb="MG MG T 501 " model vdw 2.031 2.170 nonbonded pdb=" OE2 GLU E 132 " pdb="MG MG E 501 " model vdw 2.033 2.170 nonbonded pdb=" OE2 GLU K 132 " pdb="MG MG K 501 " model vdw 2.034 2.170 nonbonded pdb=" OE2 GLU Q 132 " pdb="MG MG Q 501 " model vdw 2.034 2.170 ... (remaining 350286 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'E' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'F' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'J' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'K' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = chain 'L' selection = (chain 'Q' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'R' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'S' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'T' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'W' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) selection = (chain 'X' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 502)) } 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=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 36.190 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 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 : 0.004 0.053 42356 Z= 0.216 Angle : 0.707 10.159 57523 Z= 0.403 Chirality : 0.043 0.215 6312 Planarity : 0.004 0.041 7523 Dihedral : 13.899 89.896 15621 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 0.56 % Allowed : 0.30 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.12), residues: 5268 helix: 1.03 (0.11), residues: 2016 sheet: -0.81 (0.18), residues: 768 loop : -0.58 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 329 TYR 0.022 0.002 TYR R 371 PHE 0.026 0.002 PHE X 134 TRP 0.017 0.002 TRP Q 81 HIS 0.005 0.001 HIS W 226 Details of bonding type rmsd covalent geometry : bond 0.00431 (42356) covalent geometry : angle 0.70656 (57523) hydrogen bonds : bond 0.12874 ( 1594) hydrogen bonds : angle 5.84304 ( 4548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 940 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6620 (mp0) REVERT: B 156 ASP cc_start: 0.6106 (m-30) cc_final: 0.5889 (m-30) REVERT: B 204 LYS cc_start: 0.5125 (ttpt) cc_final: 0.4547 (mptt) REVERT: B 242 MET cc_start: 0.7798 (ttm) cc_final: 0.7175 (ttp) REVERT: B 257 TYR cc_start: 0.7560 (t80) cc_final: 0.6901 (t80) REVERT: B 319 ARG cc_start: 0.6523 (ttp80) cc_final: 0.6286 (ttt180) REVERT: E 15 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6595 (mp0) REVERT: E 230 MET cc_start: 0.6812 (ttt) cc_final: 0.6604 (ttt) REVERT: E 242 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6581 (tpp) REVERT: E 319 ARG cc_start: 0.6665 (ttt-90) cc_final: 0.6232 (ttt180) REVERT: E 358 ARG cc_start: 0.6754 (mtp180) cc_final: 0.6497 (mtm180) REVERT: F 15 GLU cc_start: 0.7335 (tp30) cc_final: 0.6752 (tp30) REVERT: F 61 ARG cc_start: 0.3728 (ptm-80) cc_final: 0.3432 (ptm-80) REVERT: F 310 SER cc_start: 0.7167 (t) cc_final: 0.6924 (p) REVERT: F 417 GLU cc_start: 0.6250 (tt0) cc_final: 0.5590 (mm-30) REVERT: F 442 TYR cc_start: 0.5971 (m-80) cc_final: 0.5736 (m-80) REVERT: J 61 ARG cc_start: 0.3793 (ptm-80) cc_final: 0.3544 (ptm-80) REVERT: J 86 ARG cc_start: 0.5667 (ttm110) cc_final: 0.4829 (ttm170) REVERT: J 221 ARG cc_start: 0.5655 (mpt90) cc_final: 0.5423 (mpt90) REVERT: J 257 TYR cc_start: 0.7595 (t80) cc_final: 0.7060 (t80) REVERT: J 319 ARG cc_start: 0.6558 (ttp80) cc_final: 0.6326 (ttt180) REVERT: J 358 ARG cc_start: 0.6709 (mtp180) cc_final: 0.6493 (mtm180) REVERT: J 398 ILE cc_start: 0.6907 (mm) cc_final: 0.6016 (pt) REVERT: J 417 GLU cc_start: 0.6329 (tt0) cc_final: 0.5783 (mm-30) REVERT: K 204 LYS cc_start: 0.4996 (ttpt) cc_final: 0.4432 (mptt) REVERT: L 15 GLU cc_start: 0.7514 (tp30) cc_final: 0.7112 (mm-30) REVERT: L 86 ARG cc_start: 0.6189 (tpp80) cc_final: 0.4848 (ttt90) REVERT: L 169 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7185 (tm-30) REVERT: L 417 GLU cc_start: 0.6282 (tt0) cc_final: 0.5640 (mp0) REVERT: L 439 LEU cc_start: 0.6518 (tp) cc_final: 0.6311 (tp) REVERT: Q 15 GLU cc_start: 0.7449 (tp30) cc_final: 0.7076 (mm-30) REVERT: Q 86 ARG cc_start: 0.6023 (tpp80) cc_final: 0.4779 (ttt90) REVERT: Q 177 MET cc_start: 0.5126 (ttm) cc_final: 0.4872 (ttm) REVERT: Q 204 LYS cc_start: 0.5171 (ttpt) cc_final: 0.4561 (mptt) REVERT: Q 310 SER cc_start: 0.7209 (t) cc_final: 0.6999 (p) REVERT: R 61 ARG cc_start: 0.3752 (ptm-80) cc_final: 0.3500 (ptm-80) REVERT: R 86 ARG cc_start: 0.6043 (tpp80) cc_final: 0.4538 (ttt90) REVERT: R 417 GLU cc_start: 0.6305 (tt0) cc_final: 0.5652 (mp0) REVERT: S 15 GLU cc_start: 0.7479 (tp30) cc_final: 0.7218 (mm-30) REVERT: S 61 ARG cc_start: 0.3748 (ptm-80) cc_final: 0.3439 (ptm-80) REVERT: S 204 LYS cc_start: 0.5329 (ttpt) cc_final: 0.4658 (mptt) REVERT: S 257 TYR cc_start: 0.7538 (t80) cc_final: 0.6904 (t80) REVERT: S 283 MET cc_start: 0.4866 (ptp) cc_final: 0.4580 (ptp) REVERT: S 324 ARG cc_start: 0.5469 (mmt-90) cc_final: 0.4597 (mmm160) REVERT: S 398 ILE cc_start: 0.6875 (mm) cc_final: 0.6017 (pt) REVERT: S 417 GLU cc_start: 0.6357 (tt0) cc_final: 0.5741 (mm-30) REVERT: T 15 GLU cc_start: 0.7401 (tp30) cc_final: 0.7117 (tp30) REVERT: T 177 MET cc_start: 0.4929 (ttm) cc_final: 0.4712 (ttm) REVERT: T 242 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6632 (tpp) REVERT: T 350 ARG cc_start: 0.6257 (tpt-90) cc_final: 0.4982 (tpp-160) REVERT: T 417 GLU cc_start: 0.6253 (tt0) cc_final: 0.5588 (mp0) REVERT: W 257 TYR cc_start: 0.7532 (t80) cc_final: 0.6970 (t80) REVERT: W 319 ARG cc_start: 0.6446 (ttp80) cc_final: 0.5894 (ttt180) REVERT: W 414 TYR cc_start: 0.5975 (m-80) cc_final: 0.5770 (m-80) REVERT: W 417 GLU cc_start: 0.6278 (tt0) cc_final: 0.5979 (mt-10) REVERT: X 15 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6794 (mm-30) REVERT: X 182 GLU cc_start: 0.7304 (tp30) cc_final: 0.7008 (tp30) REVERT: X 204 LYS cc_start: 0.4703 (ttpt) cc_final: 0.4283 (mptt) REVERT: X 242 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: X 319 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6008 (ttt180) REVERT: X 399 ARG cc_start: 0.6413 (mmt90) cc_final: 0.6068 (mtt180) outliers start: 24 outliers final: 6 residues processed: 949 average time/residue: 0.2890 time to fit residues: 428.8462 Evaluate side-chains 669 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 660 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain J residue 334 ASN Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain R residue 167 ARG Chi-restraints excluded: chain S residue 336 ASP Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain X residue 242 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.0870 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.0770 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS E 226 HIS E 246 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 193 HIS F 223 HIS J 223 HIS J 238 ASN J 246 GLN K 33 ASN K 149 ASN K 193 HIS K 223 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN L 149 ASN L 223 HIS ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 ASN Q 223 HIS Q 226 HIS R 149 ASN R 223 HIS ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 334 ASN S 223 HIS S 226 HIS S 288 ASN S 429 GLN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 223 HIS ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 238 ASN ** W 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 GLN ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 223 HIS X 226 HIS X 246 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.236198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.222466 restraints weight = 49571.067| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.25 r_work: 0.4323 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4219 r_free = 0.4219 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4219 r_free = 0.4219 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42356 Z= 0.127 Angle : 0.572 6.221 57523 Z= 0.296 Chirality : 0.042 0.151 6312 Planarity : 0.004 0.043 7523 Dihedral : 4.944 51.570 5867 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.42 % Allowed : 7.38 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5268 helix: 1.03 (0.11), residues: 2124 sheet: -0.68 (0.18), residues: 840 loop : -0.61 (0.14), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 329 TYR 0.020 0.002 TYR R 371 PHE 0.020 0.002 PHE R 212 TRP 0.008 0.001 TRP R 81 HIS 0.006 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00294 (42356) covalent geometry : angle 0.57232 (57523) hydrogen bonds : bond 0.03608 ( 1594) hydrogen bonds : angle 4.76984 ( 4548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 744 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 LYS cc_start: 0.5912 (ttpt) cc_final: 0.5323 (mptt) REVERT: E 319 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6712 (ttt180) REVERT: J 242 MET cc_start: 0.7731 (tmm) cc_final: 0.7247 (tmm) REVERT: K 15 GLU cc_start: 0.7479 (tp30) cc_final: 0.7093 (tp30) REVERT: K 204 LYS cc_start: 0.6038 (ttpt) cc_final: 0.5548 (mptt) REVERT: L 86 ARG cc_start: 0.6283 (tpp80) cc_final: 0.5797 (ttt180) REVERT: L 169 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7591 (tp30) REVERT: L 302 GLU cc_start: 0.5551 (tp30) cc_final: 0.5304 (tp30) REVERT: L 319 ARG cc_start: 0.7167 (ttt-90) cc_final: 0.6779 (ttt180) REVERT: Q 86 ARG cc_start: 0.6066 (tpp80) cc_final: 0.5828 (ttt90) REVERT: Q 204 LYS cc_start: 0.6274 (ttpt) cc_final: 0.5724 (mptt) REVERT: R 15 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7164 (mm-30) REVERT: R 204 LYS cc_start: 0.6287 (ttpt) cc_final: 0.5655 (mptt) REVERT: R 366 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5319 (mm) REVERT: S 86 ARG cc_start: 0.6171 (tpp80) cc_final: 0.5389 (ttm170) REVERT: S 169 GLU cc_start: 0.7758 (tp30) cc_final: 0.6906 (mp0) REVERT: S 204 LYS cc_start: 0.6004 (ttpt) cc_final: 0.5420 (mptt) REVERT: S 370 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4442 (tp) REVERT: T 157 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6973 (tt) REVERT: T 319 ARG cc_start: 0.7051 (ttt-90) cc_final: 0.6807 (ttp-170) REVERT: W 319 ARG cc_start: 0.6656 (ttp80) cc_final: 0.6394 (ttt180) REVERT: X 204 LYS cc_start: 0.5549 (ttpt) cc_final: 0.5027 (mptt) REVERT: X 242 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7442 (tpp) REVERT: X 319 ARG cc_start: 0.6773 (ttp80) cc_final: 0.6409 (ttt180) REVERT: X 399 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7297 (mtt180) outliers start: 61 outliers final: 35 residues processed: 759 average time/residue: 0.2871 time to fit residues: 341.9342 Evaluate side-chains 668 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 629 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 334 ASN Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 175 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 242 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 482 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 463 optimal weight: 0.7980 chunk 320 optimal weight: 7.9990 chunk 497 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 288 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN F 313 ASN K 149 ASN K 193 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 313 ASN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 313 ASN Q 429 GLN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 313 ASN ** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 245 ASN S 246 GLN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 313 ASN ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.225353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.206311 restraints weight = 51602.171| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.89 r_work: 0.4236 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 42356 Z= 0.341 Angle : 0.823 11.209 57523 Z= 0.421 Chirality : 0.051 0.231 6312 Planarity : 0.006 0.070 7523 Dihedral : 5.952 45.687 5851 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.69 % Allowed : 13.14 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.11), residues: 5268 helix: 0.41 (0.11), residues: 2052 sheet: -1.21 (0.18), residues: 804 loop : -1.23 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.029 0.003 TYR R 154 PHE 0.031 0.003 PHE L 136 TRP 0.009 0.002 TRP R 81 HIS 0.011 0.002 HIS Q 410 Details of bonding type rmsd covalent geometry : bond 0.00814 (42356) covalent geometry : angle 0.82326 (57523) hydrogen bonds : bond 0.05109 ( 1594) hydrogen bonds : angle 5.44704 ( 4548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 618 time to evaluate : 1.616 Fit side-chains REVERT: B 15 GLU cc_start: 0.7271 (tp30) cc_final: 0.6945 (tp30) REVERT: B 204 LYS cc_start: 0.6155 (ttpt) cc_final: 0.5551 (mptt) REVERT: B 257 TYR cc_start: 0.7100 (t80) cc_final: 0.6845 (t80) REVERT: E 15 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: E 204 LYS cc_start: 0.6440 (ttpt) cc_final: 0.5744 (mptt) REVERT: E 319 ARG cc_start: 0.7374 (ttt180) cc_final: 0.7136 (ttt180) REVERT: E 417 GLU cc_start: 0.7707 (tt0) cc_final: 0.7436 (mp0) REVERT: F 15 GLU cc_start: 0.7378 (tp30) cc_final: 0.7100 (tp30) REVERT: F 139 ASP cc_start: 0.6471 (p0) cc_final: 0.5692 (p0) REVERT: F 204 LYS cc_start: 0.6419 (ttpt) cc_final: 0.5739 (mptt) REVERT: F 273 MET cc_start: 0.7107 (mmp) cc_final: 0.6803 (mmt) REVERT: J 169 GLU cc_start: 0.7970 (tp30) cc_final: 0.6915 (mp0) REVERT: J 204 LYS cc_start: 0.6256 (ttpt) cc_final: 0.5624 (mptt) REVERT: J 242 MET cc_start: 0.8019 (tmm) cc_final: 0.7616 (tmm) REVERT: J 370 ILE cc_start: 0.4829 (OUTLIER) cc_final: 0.4432 (tp) REVERT: K 15 GLU cc_start: 0.7450 (tp30) cc_final: 0.7149 (tp30) REVERT: K 204 LYS cc_start: 0.6193 (ttpt) cc_final: 0.5650 (mptt) REVERT: K 417 GLU cc_start: 0.7690 (tt0) cc_final: 0.7343 (mm-30) REVERT: L 86 ARG cc_start: 0.6695 (tpp80) cc_final: 0.5731 (ttt180) REVERT: L 160 MET cc_start: 0.6149 (ptp) cc_final: 0.5785 (ptp) REVERT: L 169 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8033 (tp30) REVERT: L 204 LYS cc_start: 0.6444 (ttpt) cc_final: 0.5817 (mptt) REVERT: L 319 ARG cc_start: 0.7456 (ttt-90) cc_final: 0.6972 (ttp-170) REVERT: L 417 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6543 (mp0) REVERT: Q 86 ARG cc_start: 0.6286 (tpp80) cc_final: 0.5651 (ttt90) REVERT: Q 204 LYS cc_start: 0.6488 (ttpt) cc_final: 0.5753 (mptt) REVERT: Q 324 ARG cc_start: 0.6080 (mmt180) cc_final: 0.5879 (mmp-170) REVERT: Q 417 GLU cc_start: 0.7681 (tt0) cc_final: 0.7314 (mm-30) REVERT: R 72 ASP cc_start: 0.6132 (m-30) cc_final: 0.5853 (m-30) REVERT: R 86 ARG cc_start: 0.6257 (tpp80) cc_final: 0.5648 (ttt90) REVERT: R 157 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7063 (tt) REVERT: R 204 LYS cc_start: 0.6319 (ttpt) cc_final: 0.5787 (mptt) REVERT: R 366 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.5593 (mm) REVERT: R 417 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6534 (mp0) REVERT: S 86 ARG cc_start: 0.6470 (tpp80) cc_final: 0.5808 (ttt90) REVERT: S 204 LYS cc_start: 0.6439 (ttpt) cc_final: 0.5724 (mptt) REVERT: S 283 MET cc_start: 0.6759 (ptp) cc_final: 0.6493 (ptp) REVERT: T 157 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7094 (tt) REVERT: T 169 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7712 (tm-30) REVERT: T 204 LYS cc_start: 0.6364 (ttpt) cc_final: 0.5703 (mptt) REVERT: W 174 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.5048 (mm) REVERT: W 204 LYS cc_start: 0.5896 (ttpt) cc_final: 0.5531 (mptt) REVERT: X 61 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.3551 (ptt180) REVERT: X 204 LYS cc_start: 0.5794 (ttpt) cc_final: 0.5281 (mptt) REVERT: X 417 GLU cc_start: 0.7666 (tt0) cc_final: 0.7305 (mp0) outliers start: 115 outliers final: 75 residues processed: 685 average time/residue: 0.2814 time to fit residues: 306.3388 Evaluate side-chains 641 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 559 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 370 ILE Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 155 PHE Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 61 ARG Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 155 PHE Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 373 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 432 optimal weight: 0.0770 chunk 100 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 513 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 470 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 359 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 288 ASN E 33 ASN E 149 ASN E 193 HIS F 33 ASN F 149 ASN F 226 HIS F 334 ASN K 149 ASN K 193 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 126 ASN R 149 ASN R 226 HIS R 334 ASN S 149 ASN T 33 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 226 HIS W 33 ASN ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 ASN X 238 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.233262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.215367 restraints weight = 50833.573| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 1.89 r_work: 0.4311 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4235 r_free = 0.4235 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4235 r_free = 0.4235 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42356 Z= 0.120 Angle : 0.561 6.650 57523 Z= 0.290 Chirality : 0.042 0.178 6312 Planarity : 0.004 0.047 7523 Dihedral : 4.849 29.319 5844 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.73 % Allowed : 15.08 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 5268 helix: 0.70 (0.11), residues: 2136 sheet: -0.87 (0.18), residues: 780 loop : -0.99 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 86 TYR 0.016 0.001 TYR L 257 PHE 0.030 0.002 PHE E 212 TRP 0.005 0.001 TRP B 76 HIS 0.005 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00281 (42356) covalent geometry : angle 0.56113 (57523) hydrogen bonds : bond 0.03473 ( 1594) hydrogen bonds : angle 4.69058 ( 4548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 642 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 LYS cc_start: 0.5955 (ttpt) cc_final: 0.5396 (mptt) REVERT: E 33 ASN cc_start: 0.6475 (OUTLIER) cc_final: 0.6001 (p0) REVERT: E 148 LEU cc_start: 0.7903 (mm) cc_final: 0.7662 (mt) REVERT: F 15 GLU cc_start: 0.7300 (tp30) cc_final: 0.7003 (tp30) REVERT: F 204 LYS cc_start: 0.6129 (ttpt) cc_final: 0.5423 (mptt) REVERT: F 273 MET cc_start: 0.7044 (mmp) cc_final: 0.6568 (mmp) REVERT: J 204 LYS cc_start: 0.6116 (ttpt) cc_final: 0.5538 (mptt) REVERT: J 242 MET cc_start: 0.7814 (tmm) cc_final: 0.7439 (tmm) REVERT: K 15 GLU cc_start: 0.7553 (tp30) cc_final: 0.7205 (tp30) REVERT: K 204 LYS cc_start: 0.6090 (ttpt) cc_final: 0.5608 (mptt) REVERT: K 366 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5199 (mm) REVERT: L 86 ARG cc_start: 0.6503 (tpp80) cc_final: 0.5740 (ttt90) REVERT: L 204 LYS cc_start: 0.6253 (ttpt) cc_final: 0.5594 (mptt) REVERT: L 242 MET cc_start: 0.7881 (tmm) cc_final: 0.7670 (tmm) REVERT: L 319 ARG cc_start: 0.7331 (ttt-90) cc_final: 0.6959 (ttt180) REVERT: L 417 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6419 (mp0) REVERT: Q 86 ARG cc_start: 0.6204 (tpp80) cc_final: 0.5718 (ttt90) REVERT: Q 204 LYS cc_start: 0.6069 (ttpt) cc_final: 0.5483 (mptt) REVERT: R 15 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6803 (tp30) REVERT: R 204 LYS cc_start: 0.6260 (ttpt) cc_final: 0.5734 (mptt) REVERT: R 366 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5511 (mm) REVERT: R 417 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6383 (mp0) REVERT: S 86 ARG cc_start: 0.6490 (tpp80) cc_final: 0.5873 (ttt90) REVERT: S 148 LEU cc_start: 0.7967 (mm) cc_final: 0.7706 (mt) REVERT: S 204 LYS cc_start: 0.6133 (ttpt) cc_final: 0.5506 (mptt) REVERT: S 302 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5772 (tp30) REVERT: T 33 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5561 (p0) REVERT: T 157 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6783 (tt) REVERT: T 204 LYS cc_start: 0.6128 (ttpt) cc_final: 0.5522 (mptt) REVERT: T 366 ILE cc_start: 0.6059 (OUTLIER) cc_final: 0.5377 (mm) REVERT: W 204 LYS cc_start: 0.5828 (ttpt) cc_final: 0.5624 (mptt) REVERT: X 148 LEU cc_start: 0.7911 (mm) cc_final: 0.7651 (mt) REVERT: X 204 LYS cc_start: 0.5521 (ttpt) cc_final: 0.5003 (mptt) outliers start: 117 outliers final: 75 residues processed: 700 average time/residue: 0.2716 time to fit residues: 305.3412 Evaluate side-chains 655 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 573 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 155 PHE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 155 PHE Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 33 ASN Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 155 PHE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 296 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 213 optimal weight: 0.0980 chunk 311 optimal weight: 2.9990 chunk 392 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN F 33 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 149 ASN K 334 ASN ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 243 HIS S 149 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 HIS ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.232532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.214585 restraints weight = 50913.076| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 1.87 r_work: 0.4331 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4199 r_free = 0.4199 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4198 r_free = 0.4198 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42356 Z= 0.137 Angle : 0.571 7.139 57523 Z= 0.293 Chirality : 0.042 0.174 6312 Planarity : 0.004 0.040 7523 Dihedral : 4.788 28.141 5844 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.57 % Allowed : 15.46 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5268 helix: 0.79 (0.11), residues: 2136 sheet: -0.78 (0.19), residues: 780 loop : -0.97 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 86 TYR 0.015 0.001 TYR F 257 PHE 0.022 0.002 PHE B 212 TRP 0.006 0.001 TRP B 423 HIS 0.004 0.001 HIS W 243 Details of bonding type rmsd covalent geometry : bond 0.00326 (42356) covalent geometry : angle 0.57128 (57523) hydrogen bonds : bond 0.03566 ( 1594) hydrogen bonds : angle 4.67384 ( 4548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 602 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7260 (tp30) cc_final: 0.7052 (tp30) REVERT: B 174 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4310 (mt) REVERT: B 204 LYS cc_start: 0.5937 (ttpt) cc_final: 0.5342 (mptt) REVERT: E 15 GLU cc_start: 0.7548 (mp0) cc_final: 0.7334 (mt-10) REVERT: E 204 LYS cc_start: 0.6138 (ttpt) cc_final: 0.5456 (mptt) REVERT: E 219 ILE cc_start: 0.6537 (tp) cc_final: 0.6086 (pt) REVERT: F 15 GLU cc_start: 0.7308 (tp30) cc_final: 0.6934 (tp30) REVERT: F 204 LYS cc_start: 0.6090 (ttpt) cc_final: 0.5470 (mptt) REVERT: F 249 PHE cc_start: 0.6545 (m-80) cc_final: 0.6310 (m-80) REVERT: F 273 MET cc_start: 0.7127 (mmp) cc_final: 0.6670 (mmt) REVERT: J 204 LYS cc_start: 0.6179 (ttpt) cc_final: 0.5585 (mptt) REVERT: J 242 MET cc_start: 0.7831 (tmm) cc_final: 0.7531 (tmm) REVERT: J 366 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.4651 (mm) REVERT: K 15 GLU cc_start: 0.7575 (tp30) cc_final: 0.7202 (tp30) REVERT: K 61 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.2988 (ptt180) REVERT: K 174 LEU cc_start: 0.4831 (OUTLIER) cc_final: 0.4332 (mt) REVERT: K 366 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5210 (mm) REVERT: L 86 ARG cc_start: 0.6486 (tpp80) cc_final: 0.5434 (tpt170) REVERT: L 204 LYS cc_start: 0.6148 (ttpt) cc_final: 0.5519 (mptt) REVERT: L 242 MET cc_start: 0.7910 (tmm) cc_final: 0.7427 (tpp) REVERT: L 319 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.6954 (ttt180) REVERT: L 417 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6548 (mp0) REVERT: Q 86 ARG cc_start: 0.6144 (tpp80) cc_final: 0.5716 (ttt90) REVERT: Q 204 LYS cc_start: 0.6037 (ttpt) cc_final: 0.5465 (mptt) REVERT: R 15 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6788 (tp30) REVERT: R 157 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6782 (tt) REVERT: R 204 LYS cc_start: 0.6269 (ttpt) cc_final: 0.5709 (mptt) REVERT: R 366 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5459 (mm) REVERT: R 417 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6449 (mp0) REVERT: S 86 ARG cc_start: 0.6486 (tpp80) cc_final: 0.5881 (ttt90) REVERT: S 139 ASP cc_start: 0.5866 (OUTLIER) cc_final: 0.5533 (p0) REVERT: S 174 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4623 (mt) REVERT: S 204 LYS cc_start: 0.6191 (ttpt) cc_final: 0.5513 (mptt) REVERT: S 370 ILE cc_start: 0.5042 (OUTLIER) cc_final: 0.4693 (tp) REVERT: T 125 MET cc_start: 0.6834 (ttt) cc_final: 0.6573 (ttp) REVERT: T 157 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6766 (tt) REVERT: T 174 LEU cc_start: 0.4956 (OUTLIER) cc_final: 0.4519 (mm) REVERT: T 204 LYS cc_start: 0.6096 (ttpt) cc_final: 0.5487 (mptt) REVERT: T 366 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5368 (mm) REVERT: T 370 ILE cc_start: 0.4611 (OUTLIER) cc_final: 0.4233 (tp) REVERT: W 177 MET cc_start: 0.5629 (ttm) cc_final: 0.5357 (mmm) REVERT: W 204 LYS cc_start: 0.5820 (ttpt) cc_final: 0.5620 (mptt) REVERT: W 302 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5583 (tp30) REVERT: X 204 LYS cc_start: 0.5510 (ttpt) cc_final: 0.5004 (mptt) outliers start: 153 outliers final: 89 residues processed: 688 average time/residue: 0.2688 time to fit residues: 297.8407 Evaluate side-chains 665 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 561 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 155 PHE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 334 ASN Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 155 PHE Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain T residue 174 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 302 GLU Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 460 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 475 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 67 optimal weight: 0.0050 chunk 79 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 258 optimal weight: 0.3980 chunk 467 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 149 ASN E 223 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 149 ASN K 238 ASN ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 126 ASN S 149 ASN T 33 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 245 ASN ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.236642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.219256 restraints weight = 50888.064| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 1.88 r_work: 0.4368 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 42356 Z= 0.102 Angle : 0.521 5.945 57523 Z= 0.269 Chirality : 0.040 0.160 6312 Planarity : 0.004 0.039 7523 Dihedral : 4.398 31.164 5844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 16.65 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 5268 helix: 0.98 (0.11), residues: 2136 sheet: -0.49 (0.20), residues: 756 loop : -0.85 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 86 TYR 0.014 0.001 TYR S 257 PHE 0.022 0.001 PHE L 212 TRP 0.006 0.001 TRP E 81 HIS 0.004 0.001 HIS J 226 Details of bonding type rmsd covalent geometry : bond 0.00237 (42356) covalent geometry : angle 0.52141 (57523) hydrogen bonds : bond 0.03137 ( 1594) hydrogen bonds : angle 4.40113 ( 4548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 643 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7278 (tp30) cc_final: 0.7042 (tp30) REVERT: B 174 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4272 (mt) REVERT: B 204 LYS cc_start: 0.5843 (ttpt) cc_final: 0.5239 (mptt) REVERT: B 439 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6620 (tp) REVERT: E 219 ILE cc_start: 0.6434 (tp) cc_final: 0.6048 (pt) REVERT: F 15 GLU cc_start: 0.7325 (tp30) cc_final: 0.6971 (tp30) REVERT: F 67 MET cc_start: 0.5197 (mtt) cc_final: 0.4952 (mtt) REVERT: J 204 LYS cc_start: 0.6098 (ttpt) cc_final: 0.5502 (mptt) REVERT: J 242 MET cc_start: 0.7614 (tmm) cc_final: 0.7233 (tmm) REVERT: J 366 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4439 (mm) REVERT: K 15 GLU cc_start: 0.7555 (tp30) cc_final: 0.7187 (tp30) REVERT: K 169 GLU cc_start: 0.7891 (tp30) cc_final: 0.6769 (mp0) REVERT: K 174 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4403 (mt) REVERT: L 125 MET cc_start: 0.6305 (ttt) cc_final: 0.6037 (ttp) REVERT: L 204 LYS cc_start: 0.5971 (ttpt) cc_final: 0.5371 (mptt) REVERT: L 242 MET cc_start: 0.7799 (tmm) cc_final: 0.7589 (tmm) REVERT: L 319 ARG cc_start: 0.7183 (ttt-90) cc_final: 0.6870 (ttp-170) REVERT: L 417 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6554 (mp0) REVERT: Q 86 ARG cc_start: 0.6131 (tpp80) cc_final: 0.5763 (ttt90) REVERT: Q 204 LYS cc_start: 0.5919 (ttpt) cc_final: 0.5332 (mptt) REVERT: R 15 GLU cc_start: 0.7781 (mm-30) cc_final: 0.6866 (tp30) REVERT: R 134 PHE cc_start: 0.6595 (m-80) cc_final: 0.6040 (m-80) REVERT: R 157 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6604 (tt) REVERT: R 204 LYS cc_start: 0.6106 (ttpt) cc_final: 0.5543 (mptt) REVERT: R 366 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5860 (pt) REVERT: R 417 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6532 (mp0) REVERT: S 86 ARG cc_start: 0.6397 (tpp80) cc_final: 0.6147 (mtp85) REVERT: S 302 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5172 (tp30) REVERT: S 370 ILE cc_start: 0.4938 (OUTLIER) cc_final: 0.4685 (tp) REVERT: T 125 MET cc_start: 0.6772 (ttt) cc_final: 0.6554 (ttp) REVERT: T 366 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5300 (mm) REVERT: T 370 ILE cc_start: 0.4331 (OUTLIER) cc_final: 0.4018 (tp) REVERT: W 302 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5441 (tp30) REVERT: W 319 ARG cc_start: 0.6821 (ttp80) cc_final: 0.6526 (ttt180) REVERT: X 148 LEU cc_start: 0.7841 (mm) cc_final: 0.7541 (mt) outliers start: 135 outliers final: 75 residues processed: 726 average time/residue: 0.2649 time to fit residues: 313.7672 Evaluate side-chains 674 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 588 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 334 ASN Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 149 ASN Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 302 GLU Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 203 optimal weight: 1.9990 chunk 502 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 454 optimal weight: 5.9990 chunk 485 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 375 optimal weight: 0.3980 chunk 199 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 525 optimal weight: 5.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN E 33 ASN E 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 313 ASN K 334 ASN ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 HIS Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 149 ASN S 313 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 ASN W 313 ASN X 33 ASN X 149 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.239133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.221211 restraints weight = 50967.424| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 1.90 r_work: 0.4336 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42356 Z= 0.122 Angle : 0.548 6.601 57523 Z= 0.281 Chirality : 0.041 0.161 6312 Planarity : 0.005 0.083 7523 Dihedral : 4.499 28.111 5844 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.32 % Allowed : 17.42 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 5268 helix: 0.98 (0.11), residues: 2136 sheet: -0.58 (0.20), residues: 768 loop : -0.85 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 221 TYR 0.027 0.001 TYR X 257 PHE 0.025 0.001 PHE B 212 TRP 0.008 0.001 TRP W 76 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00289 (42356) covalent geometry : angle 0.54802 (57523) hydrogen bonds : bond 0.03350 ( 1594) hydrogen bonds : angle 4.48534 ( 4548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 587 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LEU cc_start: 0.4702 (OUTLIER) cc_final: 0.4249 (mt) REVERT: B 439 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6692 (tp) REVERT: E 33 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.5873 (p0) REVERT: E 204 LYS cc_start: 0.6107 (ttpt) cc_final: 0.5465 (mptt) REVERT: E 219 ILE cc_start: 0.6407 (tp) cc_final: 0.6055 (pt) REVERT: E 319 ARG cc_start: 0.6934 (ttt180) cc_final: 0.6580 (ttt180) REVERT: F 15 GLU cc_start: 0.7372 (tp30) cc_final: 0.6959 (tp30) REVERT: F 273 MET cc_start: 0.7042 (mmp) cc_final: 0.6603 (mmt) REVERT: J 61 ARG cc_start: 0.3623 (ptm-80) cc_final: 0.3372 (ptm-80) REVERT: J 204 LYS cc_start: 0.6127 (ttpt) cc_final: 0.5510 (mptt) REVERT: J 366 ILE cc_start: 0.5236 (OUTLIER) cc_final: 0.4518 (mm) REVERT: K 15 GLU cc_start: 0.7526 (tp30) cc_final: 0.7149 (tp30) REVERT: K 174 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4453 (mt) REVERT: L 86 ARG cc_start: 0.6846 (mmt90) cc_final: 0.5806 (mmm-85) REVERT: L 125 MET cc_start: 0.6413 (ttt) cc_final: 0.6120 (ttp) REVERT: L 242 MET cc_start: 0.7874 (tmm) cc_final: 0.7587 (tpp) REVERT: L 319 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.6924 (ttt180) REVERT: L 417 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6571 (mp0) REVERT: Q 33 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.5628 (p0) REVERT: Q 86 ARG cc_start: 0.6172 (tpp80) cc_final: 0.5727 (ttt90) REVERT: Q 204 LYS cc_start: 0.5903 (ttpt) cc_final: 0.5340 (mptt) REVERT: R 15 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6821 (tp30) REVERT: R 157 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6365 (tt) REVERT: R 366 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5197 (mm) REVERT: R 417 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6537 (mp0) REVERT: S 174 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4677 (mt) REVERT: S 302 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5229 (tp30) REVERT: S 370 ILE cc_start: 0.4919 (OUTLIER) cc_final: 0.4675 (tp) REVERT: T 125 MET cc_start: 0.6890 (ttt) cc_final: 0.6686 (ttp) REVERT: T 169 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7622 (tm-30) REVERT: T 174 LEU cc_start: 0.5020 (OUTLIER) cc_final: 0.4574 (mt) REVERT: T 366 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5287 (mm) REVERT: T 370 ILE cc_start: 0.4463 (OUTLIER) cc_final: 0.4134 (tp) REVERT: W 174 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4431 (mt) REVERT: W 319 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6702 (ttt180) REVERT: X 33 ASN cc_start: 0.6407 (OUTLIER) cc_final: 0.5948 (p0) outliers start: 142 outliers final: 91 residues processed: 677 average time/residue: 0.2692 time to fit residues: 295.8431 Evaluate side-chains 670 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 563 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 334 ASN Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 155 PHE Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 334 ASN Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 174 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 33 ASN Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 361 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 470 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 HIS K 149 ASN ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 149 ASN T 33 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN X 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.234103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.216212 restraints weight = 50899.240| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.88 r_work: 0.4322 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4203 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4243 r_free = 0.4243 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4243 r_free = 0.4243 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42356 Z= 0.132 Angle : 0.563 7.449 57523 Z= 0.288 Chirality : 0.042 0.176 6312 Planarity : 0.005 0.084 7523 Dihedral : 4.601 28.865 5844 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.46 % Allowed : 17.77 % Favored : 78.78 % 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: -0.19 (0.12), residues: 5268 helix: 0.95 (0.11), residues: 2136 sheet: -0.57 (0.20), residues: 768 loop : -0.92 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 86 TYR 0.015 0.001 TYR Q 257 PHE 0.024 0.001 PHE B 212 TRP 0.006 0.001 TRP B 76 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00316 (42356) covalent geometry : angle 0.56295 (57523) hydrogen bonds : bond 0.03444 ( 1594) hydrogen bonds : angle 4.53418 ( 4548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 576 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4397 (mt) REVERT: B 439 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6718 (tp) REVERT: E 204 LYS cc_start: 0.6135 (ttpt) cc_final: 0.5473 (mptt) REVERT: E 219 ILE cc_start: 0.6417 (tp) cc_final: 0.6035 (pt) REVERT: E 302 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5245 (tp30) REVERT: E 319 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6595 (ttt180) REVERT: F 15 GLU cc_start: 0.7311 (tp30) cc_final: 0.6939 (tp30) REVERT: F 273 MET cc_start: 0.7083 (mmp) cc_final: 0.6676 (mmp) REVERT: J 61 ARG cc_start: 0.3680 (ptm-80) cc_final: 0.3449 (ptm-80) REVERT: J 177 MET cc_start: 0.5236 (ttt) cc_final: 0.4973 (mtp) REVERT: J 204 LYS cc_start: 0.6146 (ttpt) cc_final: 0.5533 (mptt) REVERT: J 242 MET cc_start: 0.7541 (tmm) cc_final: 0.7242 (tmm) REVERT: K 15 GLU cc_start: 0.7545 (tp30) cc_final: 0.7121 (tp30) REVERT: K 174 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4307 (mt) REVERT: L 86 ARG cc_start: 0.6800 (mmt90) cc_final: 0.5413 (tpt170) REVERT: L 125 MET cc_start: 0.6421 (ttt) cc_final: 0.6131 (ttp) REVERT: L 242 MET cc_start: 0.7647 (tmm) cc_final: 0.7400 (tpp) REVERT: L 319 ARG cc_start: 0.7337 (ttt-90) cc_final: 0.6937 (ttt180) REVERT: L 417 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6635 (mp0) REVERT: Q 86 ARG cc_start: 0.6181 (tpp80) cc_final: 0.5739 (ttt90) REVERT: Q 204 LYS cc_start: 0.5897 (ttpt) cc_final: 0.5272 (mptt) REVERT: R 15 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6834 (tp30) REVERT: R 157 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6366 (tt) REVERT: R 366 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5090 (mm) REVERT: S 174 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4620 (mt) REVERT: S 302 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5250 (tp30) REVERT: T 169 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7586 (tm-30) REVERT: T 174 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4568 (mt) REVERT: T 366 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5341 (mm) REVERT: T 370 ILE cc_start: 0.4510 (OUTLIER) cc_final: 0.4149 (tp) REVERT: W 174 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4519 (mt) REVERT: W 302 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5417 (tp30) REVERT: X 33 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.6005 (p0) REVERT: X 174 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4915 (mm) outliers start: 148 outliers final: 100 residues processed: 669 average time/residue: 0.2650 time to fit residues: 289.6719 Evaluate side-chains 666 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 551 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 334 ASN Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 174 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 243 HIS Chi-restraints excluded: chain W residue 302 GLU Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 33 ASN Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 174 LEU Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 391 optimal weight: 5.9990 chunk 493 optimal weight: 4.9990 chunk 497 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 442 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 210 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN E 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN K 334 ASN L 226 HIS Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 149 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN X 149 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.233666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.215799 restraints weight = 50826.734| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 1.85 r_work: 0.4320 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42356 Z= 0.139 Angle : 0.576 7.017 57523 Z= 0.294 Chirality : 0.042 0.176 6312 Planarity : 0.005 0.075 7523 Dihedral : 4.693 29.442 5844 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.41 % Allowed : 18.26 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 5268 helix: 0.89 (0.11), residues: 2136 sheet: -0.58 (0.20), residues: 768 loop : -0.98 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 86 TYR 0.018 0.001 TYR K 257 PHE 0.024 0.002 PHE B 212 TRP 0.006 0.001 TRP T 76 HIS 0.004 0.001 HIS W 243 Details of bonding type rmsd covalent geometry : bond 0.00332 (42356) covalent geometry : angle 0.57618 (57523) hydrogen bonds : bond 0.03521 ( 1594) hydrogen bonds : angle 4.59427 ( 4548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 567 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7022 (tp30) cc_final: 0.6786 (tp30) REVERT: B 174 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4405 (mt) REVERT: B 439 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6763 (tp) REVERT: E 33 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.6259 (p0) REVERT: E 204 LYS cc_start: 0.6177 (ttpt) cc_final: 0.5523 (mptt) REVERT: E 219 ILE cc_start: 0.6417 (tp) cc_final: 0.6027 (pt) REVERT: E 302 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5266 (tp30) REVERT: E 319 ARG cc_start: 0.7017 (ttt180) cc_final: 0.6573 (ttt180) REVERT: F 15 GLU cc_start: 0.7311 (tp30) cc_final: 0.6951 (tp30) REVERT: F 66 ASP cc_start: 0.5245 (m-30) cc_final: 0.5027 (m-30) REVERT: F 273 MET cc_start: 0.7093 (mmp) cc_final: 0.6681 (mmp) REVERT: F 302 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.4226 (tp30) REVERT: J 61 ARG cc_start: 0.3711 (ptm-80) cc_final: 0.3483 (ptm-80) REVERT: J 204 LYS cc_start: 0.6080 (ttpt) cc_final: 0.5450 (mptt) REVERT: J 242 MET cc_start: 0.7621 (tmm) cc_final: 0.7273 (tmm) REVERT: K 15 GLU cc_start: 0.7519 (tp30) cc_final: 0.7109 (tp30) REVERT: K 61 ARG cc_start: 0.5178 (OUTLIER) cc_final: 0.2918 (ptt180) REVERT: K 174 LEU cc_start: 0.4847 (OUTLIER) cc_final: 0.4338 (mt) REVERT: L 86 ARG cc_start: 0.6794 (mmt90) cc_final: 0.5672 (ttt180) REVERT: L 125 MET cc_start: 0.6340 (ttt) cc_final: 0.6059 (ttp) REVERT: L 319 ARG cc_start: 0.7344 (ttt-90) cc_final: 0.6959 (ttt180) REVERT: L 417 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6645 (mp0) REVERT: Q 86 ARG cc_start: 0.6188 (tpp80) cc_final: 0.5720 (ttt90) REVERT: Q 204 LYS cc_start: 0.5926 (ttpt) cc_final: 0.5296 (mptt) REVERT: R 15 GLU cc_start: 0.7797 (mm-30) cc_final: 0.6783 (tp30) REVERT: R 86 ARG cc_start: 0.7116 (mmm-85) cc_final: 0.5740 (ttt180) REVERT: R 139 ASP cc_start: 0.6651 (p0) cc_final: 0.5560 (p0) REVERT: R 157 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6355 (tt) REVERT: R 366 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5096 (mm) REVERT: S 174 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4655 (mt) REVERT: S 302 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5252 (tp30) REVERT: T 169 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: T 174 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4530 (mt) REVERT: T 366 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5367 (mm) REVERT: T 370 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.4128 (tp) REVERT: W 174 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4445 (mt) REVERT: W 302 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5494 (tp30) REVERT: X 33 ASN cc_start: 0.6437 (OUTLIER) cc_final: 0.5972 (p0) REVERT: X 135 LEU cc_start: 0.7725 (mt) cc_final: 0.7497 (mt) outliers start: 146 outliers final: 105 residues processed: 662 average time/residue: 0.2602 time to fit residues: 282.3239 Evaluate side-chains 673 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 550 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 334 ASN Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 243 HIS Chi-restraints excluded: chain W residue 302 GLU Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 33 ASN Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 13 optimal weight: 0.8980 chunk 510 optimal weight: 1.9990 chunk 294 optimal weight: 0.4980 chunk 421 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 267 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN E 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 HIS K 149 ASN K 334 ASN Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 149 ASN R 238 ASN S 149 ASN ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.239668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.221864 restraints weight = 50785.484| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 1.89 r_work: 0.4345 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42356 Z= 0.116 Angle : 0.556 8.405 57523 Z= 0.285 Chirality : 0.041 0.165 6312 Planarity : 0.005 0.073 7523 Dihedral : 4.562 31.574 5844 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.94 % Allowed : 18.87 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 5268 helix: 0.94 (0.11), residues: 2136 sheet: -0.54 (0.20), residues: 768 loop : -0.91 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 333 TYR 0.024 0.001 TYR B 416 PHE 0.024 0.001 PHE B 212 TRP 0.005 0.001 TRP X 423 HIS 0.004 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00274 (42356) covalent geometry : angle 0.55580 (57523) hydrogen bonds : bond 0.03304 ( 1594) hydrogen bonds : angle 4.50504 ( 4548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 573 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.6304 (OUTLIER) cc_final: 0.5764 (p0) REVERT: B 174 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4353 (mt) REVERT: B 439 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6671 (tp) REVERT: E 204 LYS cc_start: 0.6157 (ttpt) cc_final: 0.5529 (mptt) REVERT: E 219 ILE cc_start: 0.6386 (tp) cc_final: 0.6017 (pt) REVERT: E 302 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5180 (tp30) REVERT: E 319 ARG cc_start: 0.7056 (ttt180) cc_final: 0.6622 (ttt180) REVERT: F 15 GLU cc_start: 0.7388 (tp30) cc_final: 0.7004 (tp30) REVERT: F 66 ASP cc_start: 0.5097 (m-30) cc_final: 0.4856 (m-30) REVERT: F 148 LEU cc_start: 0.7736 (mm) cc_final: 0.7497 (mt) REVERT: F 273 MET cc_start: 0.7010 (mmp) cc_final: 0.6631 (mmp) REVERT: F 302 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.4144 (tp30) REVERT: J 61 ARG cc_start: 0.3818 (ptm-80) cc_final: 0.3611 (ptm-80) REVERT: J 204 LYS cc_start: 0.6049 (ttpt) cc_final: 0.5423 (mptt) REVERT: J 242 MET cc_start: 0.7542 (tmm) cc_final: 0.7130 (tmm) REVERT: K 15 GLU cc_start: 0.7509 (tp30) cc_final: 0.7163 (tp30) REVERT: K 174 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4327 (mt) REVERT: L 86 ARG cc_start: 0.6764 (mmt90) cc_final: 0.5309 (tpt170) REVERT: L 125 MET cc_start: 0.6317 (ttt) cc_final: 0.6014 (ttp) REVERT: L 242 MET cc_start: 0.7673 (tmm) cc_final: 0.7402 (tpp) REVERT: L 319 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6832 (ttt180) REVERT: L 417 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6596 (mp0) REVERT: Q 86 ARG cc_start: 0.6156 (tpp80) cc_final: 0.5757 (ttt90) REVERT: Q 204 LYS cc_start: 0.5885 (ttpt) cc_final: 0.5242 (mptt) REVERT: R 15 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6791 (tp30) REVERT: R 86 ARG cc_start: 0.7041 (mmm-85) cc_final: 0.5741 (ttt180) REVERT: R 134 PHE cc_start: 0.6672 (m-80) cc_final: 0.6351 (m-80) REVERT: R 157 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6269 (tt) REVERT: R 366 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5073 (mm) REVERT: S 174 LEU cc_start: 0.4966 (OUTLIER) cc_final: 0.4594 (mt) REVERT: S 302 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5201 (tp30) REVERT: T 174 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4626 (mt) REVERT: T 366 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5335 (mm) REVERT: T 370 ILE cc_start: 0.4526 (OUTLIER) cc_final: 0.4238 (tp) REVERT: W 177 MET cc_start: 0.5625 (tpt) cc_final: 0.5349 (mmm) REVERT: W 302 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: X 135 LEU cc_start: 0.7669 (mt) cc_final: 0.7462 (mt) REVERT: X 148 LEU cc_start: 0.7737 (mm) cc_final: 0.7521 (mt) outliers start: 126 outliers final: 99 residues processed: 653 average time/residue: 0.2617 time to fit residues: 281.1690 Evaluate side-chains 666 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 553 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 334 ASN Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 33 ASN Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 302 GLU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 155 PHE Chi-restraints excluded: chain T residue 174 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 385 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 243 HIS Chi-restraints excluded: chain W residue 302 GLU Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 191 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 448 optimal weight: 5.9990 chunk 260 optimal weight: 0.0170 chunk 268 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN Q 33 ASN Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.232993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.214722 restraints weight = 51238.924| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.87 r_work: 0.4313 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42356 Z= 0.184 Angle : 0.637 8.365 57523 Z= 0.324 Chirality : 0.044 0.188 6312 Planarity : 0.005 0.086 7523 Dihedral : 4.949 28.405 5844 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.40 % Favored : 93.58 % Rotamer: Outliers : 3.22 % Allowed : 18.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 5268 helix: 0.77 (0.11), residues: 2136 sheet: -0.64 (0.20), residues: 768 loop : -1.13 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 86 TYR 0.028 0.002 TYR B 416 PHE 0.022 0.002 PHE B 212 TRP 0.009 0.001 TRP T 76 HIS 0.008 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00441 (42356) covalent geometry : angle 0.63743 (57523) hydrogen bonds : bond 0.03870 ( 1594) hydrogen bonds : angle 4.77716 ( 4548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11701.32 seconds wall clock time: 200 minutes 49.10 seconds (12049.10 seconds total)