Starting phenix.real_space_refine on Mon Jul 6 03:30:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqy_37758/07_2026/8wqy_37758.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20998 2.51 5 N 5346 2.21 5 O 6420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32860 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "D" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "E" Number of atoms: 1364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1346 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 164, 1346 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 2 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "G" Number of atoms: 1362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1350 Chain: "H" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "I" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1360 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1360 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1367 Chain: "J" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "K" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "L" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "M" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "N" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "O" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "P" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "Q" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "R" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "S" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "T" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "U" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "V" Number of atoms: 1381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1370 Chain: "W" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "X" Number of atoms: 1381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1370 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 12.19, per 1000 atoms: 0.37 Number of scatterers: 32860 At special positions: 0 Unit cell: (146.566, 145.519, 149.707, 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) Fe 24 26.01 S 72 16.00 O 6420 8.00 N 5346 7.00 C 20998 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: 2.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7706 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 12 sheets defined 83.3% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 14 through 44 Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.963A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 123 removed outlier: 3.708A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 3.785A pdb=" N PHE A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.895A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 45 removed outlier: 3.589A pdb=" N PHE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.640A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 122 removed outlier: 3.702A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.363A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.942A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 45 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.698A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 122 removed outlier: 3.523A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.708A pdb=" N PHE C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.576A pdb=" N PHE D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.386A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 122 removed outlier: 3.849A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.810A pdb=" N PHE D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.771A pdb=" N ILE D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.900A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.591A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.884A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 155 removed outlier: 3.903A pdb=" N PHE E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 155 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 removed outlier: 3.516A pdb=" N PHE F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.482A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.949A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 3.582A pdb=" N PHE F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 removed outlier: 3.984A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 156' Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.974A pdb=" N ILE F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 44 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.161A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 122 removed outlier: 3.601A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 3.652A pdb=" N PHE G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 156 removed outlier: 3.929A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 151 through 156' Processing helix chain 'G' and resid 158 through 172 removed outlier: 3.608A pdb=" N ILE G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 45 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.842A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 3.567A pdb=" N PHE H 129 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 removed outlier: 3.677A pdb=" N ILE H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 44 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.507A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.656A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 4.639A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 removed outlier: 4.249A pdb=" N ILE I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 45 removed outlier: 3.667A pdb=" N PHE J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.664A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.520A pdb=" N LEU J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 151 removed outlier: 4.562A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 44 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.848A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.551A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 3.516A pdb=" N PHE K 129 " --> pdb=" O ASP K 125 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 removed outlier: 3.519A pdb=" N ILE K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 44 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.387A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.739A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 3.660A pdb=" N PHE L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 removed outlier: 4.180A pdb=" N ILE L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 44 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.172A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 122 removed outlier: 3.618A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 removed outlier: 3.750A pdb=" N ILE M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 151 removed outlier: 3.944A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 removed outlier: 3.684A pdb=" N ILE M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 45 removed outlier: 3.517A pdb=" N PHE N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.642A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.816A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 3.625A pdb=" N PHE N 129 " --> pdb=" O ASP N 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 170 Processing helix chain 'O' and resid 14 through 44 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.575A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.583A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 3.666A pdb=" N PHE O 129 " --> pdb=" O ASP O 125 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 44 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.474A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.533A pdb=" N LEU P 98 " --> pdb=" O ASP P 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 3.740A pdb=" N PHE P 129 " --> pdb=" O ASP P 125 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 171 removed outlier: 3.664A pdb=" N ILE P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 45 removed outlier: 3.626A pdb=" N PHE Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.484A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 122 Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.428A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 removed outlier: 3.730A pdb=" N PHE R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.508A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.714A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.373A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 172 removed outlier: 3.709A pdb=" N ILE R 162 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS R 172 " --> pdb=" O GLU R 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 44 Processing helix chain 'S' and resid 47 through 63 removed outlier: 3.507A pdb=" N GLY S 51 " --> pdb=" O MET S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.437A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.617A pdb=" N LEU S 98 " --> pdb=" O ASP S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.927A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 44 removed outlier: 3.524A pdb=" N HIS T 36 " --> pdb=" O LEU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.499A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.524A pdb=" N VAL T 109 " --> pdb=" O ARG T 105 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG T 110 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU T 123 " --> pdb=" O LEU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 3.592A pdb=" N PHE T 129 " --> pdb=" O ASP T 125 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 removed outlier: 3.575A pdb=" N SER T 155 " --> pdb=" O LEU T 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 152 through 155' Processing helix chain 'T' and resid 158 through 171 removed outlier: 3.646A pdb=" N ILE T 162 " --> pdb=" O ASP T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 45 removed outlier: 3.576A pdb=" N PHE U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 5.062A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.551A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 3.749A pdb=" N PHE U 129 " --> pdb=" O ASP U 125 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 44 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.285A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.670A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 3.966A pdb=" N PHE V 129 " --> pdb=" O ASP V 125 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 172 removed outlier: 3.863A pdb=" N ILE V 162 " --> pdb=" O ASP V 158 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS V 172 " --> pdb=" O GLU V 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 45 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.767A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 123 removed outlier: 3.562A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 3.583A pdb=" N PHE W 129 " --> pdb=" O ASP W 125 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 171 removed outlier: 3.589A pdb=" N ILE W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 44 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.661A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.661A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU X 123 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.572A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2573 hydrogen bonds defined for protein. 7701 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: 5.69 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5888 1.30 - 1.43: 8627 1.43 - 1.55: 18861 1.55 - 1.68: 0 1.68 - 1.80: 144 Bond restraints: 33520 Sorted by residual: bond pdb=" CA ASP V 125 " pdb=" C ASP V 125 " ideal model delta sigma weight residual 1.521 1.437 0.085 1.17e-02 7.31e+03 5.22e+01 bond pdb=" CA GLN E 133 " pdb=" C GLN E 133 " ideal model delta sigma weight residual 1.525 1.453 0.072 1.38e-02 5.25e+03 2.73e+01 bond pdb=" CA TRP E 134 " pdb=" C TRP E 134 " ideal model delta sigma weight residual 1.519 1.459 0.060 1.22e-02 6.72e+03 2.40e+01 bond pdb=" CA ASP T 125 " pdb=" C ASP T 125 " ideal model delta sigma weight residual 1.526 1.465 0.062 1.35e-02 5.49e+03 2.08e+01 bond pdb=" CA HIS T 36 " pdb=" C HIS T 36 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.37e-02 5.33e+03 1.97e+01 ... (remaining 33515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 45128 3.11 - 6.22: 146 6.22 - 9.33: 6 9.33 - 12.45: 3 12.45 - 15.56: 1 Bond angle restraints: 45284 Sorted by residual: angle pdb=" N TRP E 134 " pdb=" CA TRP E 134 " pdb=" C TRP E 134 " ideal model delta sigma weight residual 113.55 97.99 15.56 1.26e+00 6.30e-01 1.52e+02 angle pdb=" N HIS T 36 " pdb=" CA HIS T 36 " pdb=" C HIS T 36 " ideal model delta sigma weight residual 112.45 100.82 11.63 1.39e+00 5.18e-01 7.00e+01 angle pdb=" N PHE M 129 " pdb=" CA PHE M 129 " pdb=" C PHE M 129 " ideal model delta sigma weight residual 113.97 105.18 8.79 1.28e+00 6.10e-01 4.72e+01 angle pdb=" N VAL T 109 " pdb=" CA VAL T 109 " pdb=" C VAL T 109 " ideal model delta sigma weight residual 110.53 104.14 6.39 9.40e-01 1.13e+00 4.62e+01 angle pdb=" N ASN T 107 " pdb=" CA ASN T 107 " pdb=" C ASN T 107 " ideal model delta sigma weight residual 113.72 105.10 8.62 1.30e+00 5.92e-01 4.40e+01 ... (remaining 45279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 18157 18.06 - 36.12: 1586 36.12 - 54.17: 255 54.17 - 72.23: 81 72.23 - 90.29: 45 Dihedral angle restraints: 20124 sinusoidal: 8182 harmonic: 11942 Sorted by residual: dihedral pdb=" C ASP V 125 " pdb=" N ASP V 125 " pdb=" CA ASP V 125 " pdb=" CB ASP V 125 " ideal model delta harmonic sigma weight residual -122.60 -110.05 -12.55 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" C TYR T 126 " pdb=" N TYR T 126 " pdb=" CA TYR T 126 " pdb=" CB TYR T 126 " ideal model delta harmonic sigma weight residual -122.60 -133.20 10.60 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C ASP T 125 " pdb=" N ASP T 125 " pdb=" CA ASP T 125 " pdb=" CB ASP T 125 " ideal model delta harmonic sigma weight residual -122.60 -112.61 -9.99 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 20121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4808 0.105 - 0.210: 92 0.210 - 0.315: 4 0.315 - 0.420: 4 0.420 - 0.525: 1 Chirality restraints: 4909 Sorted by residual: chirality pdb=" CA TYR T 126 " pdb=" N TYR T 126 " pdb=" C TYR T 126 " pdb=" CB TYR T 126 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA TYR M 126 " pdb=" N TYR M 126 " pdb=" C TYR M 126 " pdb=" CB TYR M 126 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASP V 124 " pdb=" N ASP V 124 " pdb=" C ASP V 124 " pdb=" CB ASP V 124 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4906 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AGLU T 108 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C AGLU T 108 " 0.070 2.00e-02 2.50e+03 pdb=" O AGLU T 108 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL T 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 99 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C ILE T 99 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE T 99 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN T 100 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS T 25 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LYS T 25 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS T 25 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU T 26 " -0.013 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 138 2.49 - 3.10: 22987 3.10 - 3.70: 47868 3.70 - 4.30: 69069 4.30 - 4.90: 118175 Nonbonded interactions: 258237 Sorted by model distance: nonbonded pdb=" OD2 ASP V 138 " pdb="FE FE V 201 " model vdw 1.893 3.000 nonbonded pdb=" OD2 ASP O 138 " pdb="FE FE O 201 " model vdw 1.930 3.000 nonbonded pdb=" OD2 ASP G 142 " pdb="FE FE G 201 " model vdw 1.935 3.000 nonbonded pdb="FE FE F 201 " pdb=" O HOH F 302 " model vdw 1.958 3.000 nonbonded pdb=" OD2 ASP G 138 " pdb="FE FE G 201 " model vdw 1.964 3.000 ... (remaining 258232 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 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 176 or resid 178 through 181)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) } 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=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.140 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.006 0.085 33520 Z= 0.302 Angle : 0.593 15.556 45284 Z= 0.364 Chirality : 0.044 0.525 4909 Planarity : 0.003 0.047 5825 Dihedral : 14.605 90.291 12418 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.01 % Allowed : 2.66 % Favored : 96.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.11), residues: 3995 helix: 0.00 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.76 (0.13), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 110 TYR 0.019 0.002 TYR A 37 PHE 0.014 0.002 PHE A 129 TRP 0.012 0.001 TRP D 134 HIS 0.007 0.001 HIS W 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.30 (33520) covalent geometry : angle 0.59294 / 0.36 (45284) hydrogen bonds : bond 0.13373 / 9.09 ( 2573) hydrogen bonds : angle 4.73876 / 3.39 ( 7701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 541 time to evaluate : 1.342 Fit side-chains REVERT: A 114 LYS cc_start: 0.7220 (ttmt) cc_final: 0.7020 (tttp) REVERT: A 141 LYS cc_start: 0.7960 (tttt) cc_final: 0.7397 (ttpt) REVERT: B 107 ASN cc_start: 0.8885 (t0) cc_final: 0.8488 (m-40) REVERT: C 111 ASP cc_start: 0.7803 (t0) cc_final: 0.7442 (t0) REVERT: D 163 GLU cc_start: 0.7696 (mp0) cc_final: 0.7235 (mp0) REVERT: F 67 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 59 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6937 (mt-10) REVERT: G 67 GLU cc_start: 0.7471 (tp30) cc_final: 0.7203 (mm-30) REVERT: G 105 ARG cc_start: 0.7554 (mmt90) cc_final: 0.7083 (mmp80) REVERT: G 157 ASN cc_start: 0.7722 (p0) cc_final: 0.7449 (m-40) REVERT: H 85 SER cc_start: 0.8902 (p) cc_final: 0.8635 (t) REVERT: H 125 ASP cc_start: 0.8169 (t70) cc_final: 0.7907 (t0) REVERT: I 22 GLN cc_start: 0.7511 (mm110) cc_final: 0.7056 (mt0) REVERT: I 81 LYS cc_start: 0.7748 (mttt) cc_final: 0.7424 (mmtp) REVERT: J 22 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7675 (mm-40) REVERT: K 56 HIS cc_start: 0.7162 (m-70) cc_final: 0.6684 (t70) REVERT: M 67 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7741 (mp0) REVERT: M 101 GLU cc_start: 0.7125 (tp30) cc_final: 0.6777 (mm-30) REVERT: N 125 ASP cc_start: 0.8630 (t70) cc_final: 0.8366 (t0) REVERT: O 22 GLN cc_start: 0.8039 (tp40) cc_final: 0.7798 (mm-40) REVERT: O 105 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7240 (mmp80) REVERT: P 22 GLN cc_start: 0.7873 (mm110) cc_final: 0.7642 (mt0) REVERT: P 71 ASP cc_start: 0.8166 (t0) cc_final: 0.7850 (t0) REVERT: Q 22 GLN cc_start: 0.8068 (mm110) cc_final: 0.7728 (tt0) REVERT: Q 148 ASP cc_start: 0.8274 (t0) cc_final: 0.8006 (t0) REVERT: R 137 ARG cc_start: 0.8234 (ttp80) cc_final: 0.8031 (ttm170) REVERT: S 56 HIS cc_start: 0.7599 (m-70) cc_final: 0.7173 (t-90) REVERT: S 148 ASP cc_start: 0.7811 (m-30) cc_final: 0.7321 (m-30) REVERT: T 78 MET cc_start: 0.8081 (mtt) cc_final: 0.7762 (mtt) REVERT: T 105 ARG cc_start: 0.7565 (mmt90) cc_final: 0.6911 (mtp85) REVERT: T 106 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8448 (tp30) REVERT: T 148 ASP cc_start: 0.7889 (t0) cc_final: 0.7665 (t0) REVERT: V 14 ASN cc_start: 0.7137 (t0) cc_final: 0.6445 (t0) REVERT: V 18 ASP cc_start: 0.7667 (m-30) cc_final: 0.7325 (m-30) REVERT: W 47 MET cc_start: 0.9028 (mtp) cc_final: 0.8752 (mtt) REVERT: W 56 HIS cc_start: 0.7972 (m-70) cc_final: 0.7747 (m90) REVERT: X 56 HIS cc_start: 0.7223 (t-90) cc_final: 0.6486 (t-90) outliers start: 4 outliers final: 3 residues processed: 544 average time/residue: 0.6864 time to fit residues: 444.6165 Evaluate side-chains 343 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain S residue 111 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN B 17 ASN C 22 GLN C 154 ASN D 17 ASN D 55 GLN D 65 HIS D 154 ASN E 17 ASN F 107 ASN G 22 GLN G 154 ASN J 36 HIS J 154 ASN K 17 ASN K 65 HIS K 177 HIS M 17 ASN N 154 ASN O 17 ASN P 17 ASN P 56 HIS P 76 ASN Q 22 GLN Q 56 HIS R 17 ASN R 23 HIS R 39 HIS R 154 ASN S 154 ASN T 14 ASN T 17 ASN T 154 ASN U 14 ASN U 39 HIS V 17 ASN V 100 GLN W 154 ASN X 17 ASN X 100 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102938 restraints weight = 318184.323| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 5.28 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33520 Z= 0.135 Angle : 0.472 7.552 45284 Z= 0.268 Chirality : 0.038 0.178 4909 Planarity : 0.003 0.042 5825 Dihedral : 3.956 61.356 4339 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.80 % Allowed : 9.90 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 3995 helix: 1.63 (0.09), residues: 3105 sheet: None (None), residues: 0 loop : -1.95 (0.16), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 75 TYR 0.017 0.001 TYR A 130 PHE 0.012 0.001 PHE A 129 TRP 0.008 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (33520) covalent geometry : angle 0.47220 / 0.27 (45284) hydrogen bonds : bond 0.06203 / 4.15 ( 2573) hydrogen bonds : angle 3.45985 / 2.47 ( 7701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 470 time to evaluate : 1.274 Fit side-chains REVERT: A 141 LYS cc_start: 0.8036 (tttt) cc_final: 0.7590 (ttpt) REVERT: B 107 ASN cc_start: 0.8983 (t0) cc_final: 0.8672 (m-40) REVERT: B 148 ASP cc_start: 0.8458 (m-30) cc_final: 0.7890 (m-30) REVERT: C 78 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: C 111 ASP cc_start: 0.7822 (t0) cc_final: 0.7569 (t70) REVERT: D 68 TYR cc_start: 0.8679 (m-10) cc_final: 0.8456 (m-10) REVERT: F 67 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7843 (tm-30) REVERT: F 101 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6520 (mm-30) REVERT: F 125 ASP cc_start: 0.8421 (t0) cc_final: 0.7872 (t0) REVERT: G 59 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7386 (mt-10) REVERT: G 67 GLU cc_start: 0.7567 (tp30) cc_final: 0.7251 (mm-30) REVERT: G 148 ASP cc_start: 0.8187 (t0) cc_final: 0.7963 (m-30) REVERT: G 157 ASN cc_start: 0.7598 (p0) cc_final: 0.7384 (m-40) REVERT: I 22 GLN cc_start: 0.7548 (mm110) cc_final: 0.7120 (mt0) REVERT: I 81 LYS cc_start: 0.7857 (mttt) cc_final: 0.7554 (mmtp) REVERT: J 106 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8590 (mm-30) REVERT: K 56 HIS cc_start: 0.7352 (m-70) cc_final: 0.6870 (t70) REVERT: L 141 LYS cc_start: 0.7075 (tttt) cc_final: 0.6828 (ttpt) REVERT: M 56 HIS cc_start: 0.7401 (t-90) cc_final: 0.7116 (t-90) REVERT: N 125 ASP cc_start: 0.8575 (t70) cc_final: 0.8294 (t0) REVERT: O 105 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7260 (mmp80) REVERT: Q 22 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7876 (tt0) REVERT: Q 148 ASP cc_start: 0.8321 (t0) cc_final: 0.8019 (t0) REVERT: R 81 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8423 (mtpm) REVERT: S 56 HIS cc_start: 0.7588 (m-70) cc_final: 0.7231 (t-90) REVERT: S 148 ASP cc_start: 0.7775 (m-30) cc_final: 0.7306 (m-30) REVERT: S 163 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8184 (mm-30) REVERT: T 22 GLN cc_start: 0.8186 (tt0) cc_final: 0.7977 (tt0) REVERT: T 34 TYR cc_start: 0.8792 (m-10) cc_final: 0.8569 (m-10) REVERT: T 78 MET cc_start: 0.8235 (mtt) cc_final: 0.7927 (mtt) REVERT: V 67 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7466 (tm-30) REVERT: V 116 ILE cc_start: 0.8277 (mt) cc_final: 0.7895 (mm) REVERT: W 164 GLU cc_start: 0.7055 (tt0) cc_final: 0.6277 (mt-10) REVERT: X 56 HIS cc_start: 0.7104 (t-90) cc_final: 0.6495 (t-90) outliers start: 33 outliers final: 15 residues processed: 488 average time/residue: 0.5921 time to fit residues: 352.3276 Evaluate side-chains 374 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 357 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain T residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 265 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 HIS B 55 GLN G 27 ASN H 39 HIS ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 HIS L 23 HIS L 39 HIS M 76 ASN Q 36 HIS Q 56 HIS Q 76 ASN Q 100 GLN S 27 ASN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 HIS W 22 GLN W 154 ASN X 154 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096331 restraints weight = 338753.558| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 5.21 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33520 Z= 0.193 Angle : 0.517 6.687 45284 Z= 0.293 Chirality : 0.040 0.175 4909 Planarity : 0.003 0.042 5825 Dihedral : 3.765 15.252 4334 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.52 % Allowed : 11.78 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 3995 helix: 1.87 (0.09), residues: 3145 sheet: None (None), residues: 0 loop : -1.95 (0.16), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 137 TYR 0.021 0.002 TYR H 126 PHE 0.013 0.001 PHE Q 53 TRP 0.008 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (33520) covalent geometry : angle 0.51680 / 0.29 (45284) hydrogen bonds : bond 0.08077 / 5.39 ( 2573) hydrogen bonds : angle 3.65648 / 2.61 ( 7701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 366 time to evaluate : 1.312 Fit side-chains REVERT: A 106 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 107 ASN cc_start: 0.8769 (t0) cc_final: 0.8559 (t0) REVERT: A 141 LYS cc_start: 0.8185 (tttt) cc_final: 0.7718 (ttpt) REVERT: B 107 ASN cc_start: 0.9030 (t0) cc_final: 0.8766 (m-40) REVERT: B 148 ASP cc_start: 0.8642 (m-30) cc_final: 0.8086 (m-30) REVERT: C 78 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: C 111 ASP cc_start: 0.8030 (t0) cc_final: 0.7782 (t0) REVERT: D 68 TYR cc_start: 0.8838 (m-10) cc_final: 0.8495 (m-10) REVERT: F 67 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7952 (tm-30) REVERT: F 125 ASP cc_start: 0.8292 (t0) cc_final: 0.7751 (t0) REVERT: F 137 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8260 (ttp80) REVERT: G 59 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7501 (mt-10) REVERT: G 67 GLU cc_start: 0.7590 (tp30) cc_final: 0.7346 (mm-30) REVERT: G 100 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: G 148 ASP cc_start: 0.8280 (t0) cc_final: 0.8056 (m-30) REVERT: I 22 GLN cc_start: 0.7607 (mm110) cc_final: 0.7239 (mt0) REVERT: I 81 LYS cc_start: 0.7997 (mttt) cc_final: 0.7724 (mmtp) REVERT: K 56 HIS cc_start: 0.7537 (m-70) cc_final: 0.7047 (t70) REVERT: L 125 ASP cc_start: 0.8583 (t70) cc_final: 0.7931 (t70) REVERT: L 141 LYS cc_start: 0.7383 (tttt) cc_final: 0.7023 (ttpt) REVERT: M 101 GLU cc_start: 0.7327 (tp30) cc_final: 0.7051 (mm-30) REVERT: N 125 ASP cc_start: 0.8650 (t0) cc_final: 0.8345 (t0) REVERT: O 105 ARG cc_start: 0.8096 (mmt90) cc_final: 0.7330 (mmp80) REVERT: Q 22 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7946 (tt0) REVERT: Q 148 ASP cc_start: 0.8346 (t0) cc_final: 0.8086 (t0) REVERT: S 56 HIS cc_start: 0.7781 (m-70) cc_final: 0.7385 (t-90) REVERT: S 71 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7969 (t70) REVERT: S 148 ASP cc_start: 0.7914 (m-30) cc_final: 0.7476 (m-30) REVERT: T 75 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7760 (mtt90) REVERT: T 78 MET cc_start: 0.8510 (mtt) cc_final: 0.8185 (mtt) REVERT: V 67 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7596 (tm-30) REVERT: W 164 GLU cc_start: 0.7116 (tt0) cc_final: 0.6301 (mt-10) REVERT: X 56 HIS cc_start: 0.7259 (t-90) cc_final: 0.6676 (t-90) outliers start: 58 outliers final: 30 residues processed: 403 average time/residue: 0.6163 time to fit residues: 301.8321 Evaluate side-chains 375 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 75 ARG Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 338 optimal weight: 7.9990 chunk 356 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 56 HIS Q 154 ASN W 22 GLN W 154 ASN X 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096321 restraints weight = 307570.286| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.02 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33520 Z= 0.191 Angle : 0.507 5.989 45284 Z= 0.289 Chirality : 0.040 0.189 4909 Planarity : 0.003 0.040 5825 Dihedral : 3.784 15.874 4334 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.64 % Allowed : 12.79 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.13), residues: 3995 helix: 2.03 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -1.79 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 137 TYR 0.019 0.002 TYR N 72 PHE 0.012 0.001 PHE A 129 TRP 0.011 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (33520) covalent geometry : angle 0.50725 / 0.29 (45284) hydrogen bonds : bond 0.08069 / 5.39 ( 2573) hydrogen bonds : angle 3.64711 / 2.60 ( 7701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 355 time to evaluate : 1.358 Fit side-chains REVERT: A 141 LYS cc_start: 0.8244 (tttt) cc_final: 0.7831 (ttpt) REVERT: B 107 ASN cc_start: 0.9095 (t0) cc_final: 0.8828 (m-40) REVERT: C 78 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: C 111 ASP cc_start: 0.7988 (t0) cc_final: 0.7731 (t0) REVERT: D 68 TYR cc_start: 0.8903 (m-10) cc_final: 0.8602 (m-10) REVERT: F 125 ASP cc_start: 0.8316 (t0) cc_final: 0.7791 (t70) REVERT: F 137 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8312 (ttp80) REVERT: G 59 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7487 (mt-10) REVERT: G 67 GLU cc_start: 0.7565 (tp30) cc_final: 0.7259 (mm-30) REVERT: G 71 ASP cc_start: 0.8224 (m-30) cc_final: 0.7841 (m-30) REVERT: G 148 ASP cc_start: 0.8240 (t0) cc_final: 0.8025 (m-30) REVERT: I 22 GLN cc_start: 0.7636 (mm110) cc_final: 0.7275 (mt0) REVERT: I 81 LYS cc_start: 0.8052 (mttt) cc_final: 0.7819 (mmtp) REVERT: K 56 HIS cc_start: 0.7594 (m-70) cc_final: 0.7128 (t70) REVERT: L 125 ASP cc_start: 0.8596 (t70) cc_final: 0.7999 (t70) REVERT: L 141 LYS cc_start: 0.7416 (tttt) cc_final: 0.7085 (ttpt) REVERT: M 101 GLU cc_start: 0.7354 (tp30) cc_final: 0.7093 (mm-30) REVERT: N 125 ASP cc_start: 0.8618 (t0) cc_final: 0.8354 (t0) REVERT: O 105 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7395 (mmp80) REVERT: Q 78 MET cc_start: 0.8314 (mtt) cc_final: 0.7971 (mtt) REVERT: Q 148 ASP cc_start: 0.8294 (t0) cc_final: 0.7985 (t0) REVERT: Q 169 MET cc_start: 0.7904 (ttm) cc_final: 0.7543 (ttm) REVERT: R 89 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8437 (mmtm) REVERT: S 15 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7740 (mmtt) REVERT: S 47 MET cc_start: 0.7996 (mtt) cc_final: 0.7009 (mmt) REVERT: S 56 HIS cc_start: 0.7912 (m-70) cc_final: 0.7478 (t70) REVERT: S 71 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8152 (t70) REVERT: S 148 ASP cc_start: 0.7931 (m-30) cc_final: 0.7493 (m-30) REVERT: T 75 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7855 (mtt90) REVERT: T 78 MET cc_start: 0.8573 (mtt) cc_final: 0.8249 (mtt) REVERT: V 14 ASN cc_start: 0.6793 (t0) cc_final: 0.5936 (t0) REVERT: V 67 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7572 (tm-30) REVERT: W 164 GLU cc_start: 0.7044 (tt0) cc_final: 0.6267 (mt-10) REVERT: X 56 HIS cc_start: 0.7175 (t-90) cc_final: 0.6622 (t-90) outliers start: 63 outliers final: 35 residues processed: 396 average time/residue: 0.5973 time to fit residues: 288.7650 Evaluate side-chains 371 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 275 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 22 GLN V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099279 restraints weight = 353572.138| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 5.33 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33520 Z= 0.147 Angle : 0.466 6.064 45284 Z= 0.265 Chirality : 0.038 0.168 4909 Planarity : 0.003 0.039 5825 Dihedral : 3.685 15.840 4334 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.27 % Allowed : 13.94 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.13), residues: 3995 helix: 2.31 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -1.62 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 137 TYR 0.019 0.001 TYR R 103 PHE 0.012 0.001 PHE Q 53 TRP 0.011 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (33520) covalent geometry : angle 0.46573 / 0.27 (45284) hydrogen bonds : bond 0.06872 / 4.58 ( 2573) hydrogen bonds : angle 3.41142 / 2.44 ( 7701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 366 time to evaluate : 1.323 Fit side-chains REVERT: A 106 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 141 LYS cc_start: 0.8200 (tttt) cc_final: 0.7873 (tmmt) REVERT: B 107 ASN cc_start: 0.9078 (t0) cc_final: 0.8804 (m-40) REVERT: D 68 TYR cc_start: 0.8894 (m-10) cc_final: 0.8562 (m-10) REVERT: F 67 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 125 ASP cc_start: 0.8283 (t0) cc_final: 0.7729 (t0) REVERT: F 137 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8231 (ttp80) REVERT: G 59 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7531 (mt-10) REVERT: G 67 GLU cc_start: 0.7583 (tp30) cc_final: 0.7327 (mm-30) REVERT: I 22 GLN cc_start: 0.7607 (mm110) cc_final: 0.7241 (mt0) REVERT: I 81 LYS cc_start: 0.8036 (mttt) cc_final: 0.7807 (mmtp) REVERT: I 110 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8130 (mmm-85) REVERT: I 164 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: K 56 HIS cc_start: 0.7509 (m-70) cc_final: 0.7079 (t70) REVERT: L 79 LYS cc_start: 0.8346 (mptt) cc_final: 0.7780 (ptpt) REVERT: L 141 LYS cc_start: 0.7320 (tttt) cc_final: 0.7101 (ttpt) REVERT: M 56 HIS cc_start: 0.7532 (t-90) cc_final: 0.7220 (t-90) REVERT: M 123 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7440 (tm-30) REVERT: M 164 GLU cc_start: 0.6908 (tt0) cc_final: 0.6667 (tp30) REVERT: N 125 ASP cc_start: 0.8538 (t0) cc_final: 0.8257 (t0) REVERT: O 105 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7299 (mmp80) REVERT: Q 78 MET cc_start: 0.8165 (mtt) cc_final: 0.7824 (mtt) REVERT: Q 148 ASP cc_start: 0.8313 (t0) cc_final: 0.8000 (t0) REVERT: Q 169 MET cc_start: 0.7831 (ttm) cc_final: 0.7379 (ttm) REVERT: R 89 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8451 (mmtm) REVERT: S 15 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7670 (mmtt) REVERT: S 47 MET cc_start: 0.7916 (mtt) cc_final: 0.6921 (mmt) REVERT: S 56 HIS cc_start: 0.7811 (m-70) cc_final: 0.7372 (t70) REVERT: S 148 ASP cc_start: 0.7853 (m-30) cc_final: 0.7423 (m-30) REVERT: T 78 MET cc_start: 0.8524 (mtt) cc_final: 0.8191 (mtt) REVERT: T 125 ASP cc_start: 0.8399 (t70) cc_final: 0.8070 (t70) REVERT: V 67 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7576 (tm-30) REVERT: V 116 ILE cc_start: 0.8444 (mt) cc_final: 0.8096 (mm) REVERT: W 164 GLU cc_start: 0.7126 (tt0) cc_final: 0.6385 (mt-10) REVERT: X 56 HIS cc_start: 0.7096 (t-90) cc_final: 0.6585 (t-90) outliers start: 48 outliers final: 32 residues processed: 398 average time/residue: 0.6106 time to fit residues: 295.5379 Evaluate side-chains 378 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 338 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 HIS V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097296 restraints weight = 316835.082| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.12 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33520 Z= 0.176 Angle : 0.489 5.713 45284 Z= 0.278 Chirality : 0.039 0.172 4909 Planarity : 0.003 0.042 5825 Dihedral : 3.706 15.386 4334 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.44 % Allowed : 14.67 % Favored : 82.89 % 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: 2.31 (0.13), residues: 3995 helix: 2.30 (0.09), residues: 3146 sheet: None (None), residues: 0 loop : -1.55 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 137 TYR 0.018 0.002 TYR N 72 PHE 0.014 0.001 PHE Q 53 TRP 0.012 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (33520) covalent geometry : angle 0.48903 / 0.28 (45284) hydrogen bonds : bond 0.07598 / 5.07 ( 2573) hydrogen bonds : angle 3.52619 / 2.52 ( 7701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 1.351 Fit side-chains REVERT: A 106 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 141 LYS cc_start: 0.8165 (tttt) cc_final: 0.7802 (tmmt) REVERT: B 107 ASN cc_start: 0.9033 (t0) cc_final: 0.8754 (m-40) REVERT: B 125 ASP cc_start: 0.8510 (t0) cc_final: 0.7747 (t70) REVERT: C 78 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: D 68 TYR cc_start: 0.8862 (m-10) cc_final: 0.8536 (m-10) REVERT: E 172 LYS cc_start: 0.7612 (tptt) cc_final: 0.6536 (tppt) REVERT: F 67 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7973 (tm-30) REVERT: F 125 ASP cc_start: 0.8302 (t0) cc_final: 0.7720 (t70) REVERT: G 59 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7414 (mt-10) REVERT: G 67 GLU cc_start: 0.7630 (tp30) cc_final: 0.7392 (mm-30) REVERT: I 22 GLN cc_start: 0.7618 (mm110) cc_final: 0.7238 (mt0) REVERT: I 78 MET cc_start: 0.8497 (mtt) cc_final: 0.8039 (mtt) REVERT: I 81 LYS cc_start: 0.8007 (mttt) cc_final: 0.7750 (mmtp) REVERT: I 164 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6139 (tt0) REVERT: K 56 HIS cc_start: 0.7542 (m-70) cc_final: 0.7051 (t70) REVERT: L 79 LYS cc_start: 0.8327 (mptt) cc_final: 0.7717 (ptpt) REVERT: L 125 ASP cc_start: 0.8556 (t70) cc_final: 0.7897 (t70) REVERT: L 141 LYS cc_start: 0.7274 (tttt) cc_final: 0.6944 (ttpt) REVERT: M 56 HIS cc_start: 0.7523 (t-90) cc_final: 0.7205 (t-90) REVERT: M 101 GLU cc_start: 0.7327 (tp30) cc_final: 0.7062 (mm-30) REVERT: M 123 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7467 (tm-30) REVERT: M 137 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8241 (ttp80) REVERT: M 164 GLU cc_start: 0.6933 (tt0) cc_final: 0.6659 (tp30) REVERT: N 125 ASP cc_start: 0.8620 (t0) cc_final: 0.8255 (t0) REVERT: O 105 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7330 (mmp80) REVERT: Q 78 MET cc_start: 0.8218 (mtt) cc_final: 0.7877 (mtt) REVERT: Q 148 ASP cc_start: 0.8256 (t0) cc_final: 0.7928 (t0) REVERT: Q 169 MET cc_start: 0.7835 (ttm) cc_final: 0.7380 (ttm) REVERT: R 89 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8447 (mmtm) REVERT: S 15 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7682 (mmtt) REVERT: S 47 MET cc_start: 0.7998 (mtt) cc_final: 0.6958 (mmt) REVERT: S 56 HIS cc_start: 0.7881 (m-70) cc_final: 0.7411 (t70) REVERT: S 148 ASP cc_start: 0.7865 (m-30) cc_final: 0.7430 (m-30) REVERT: T 125 ASP cc_start: 0.8460 (t70) cc_final: 0.8129 (t70) REVERT: V 67 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7546 (tm-30) REVERT: V 116 ILE cc_start: 0.8391 (mt) cc_final: 0.8009 (mm) REVERT: W 164 GLU cc_start: 0.7156 (tt0) cc_final: 0.6384 (mt-10) REVERT: X 56 HIS cc_start: 0.7102 (t-90) cc_final: 0.6545 (t-90) outliers start: 54 outliers final: 39 residues processed: 380 average time/residue: 0.6029 time to fit residues: 278.1048 Evaluate side-chains 375 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 333 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 157 ASN Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 5 optimal weight: 0.0870 chunk 280 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN M 154 ASN Q 56 HIS V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105391 restraints weight = 338624.534| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.32 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33520 Z= 0.116 Angle : 0.429 6.354 45284 Z= 0.244 Chirality : 0.037 0.161 4909 Planarity : 0.003 0.039 5825 Dihedral : 3.546 14.546 4334 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.91 % Allowed : 15.34 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.13), residues: 3995 helix: 2.70 (0.09), residues: 3121 sheet: None (None), residues: 0 loop : -1.12 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 137 TYR 0.019 0.001 TYR R 103 PHE 0.012 0.001 PHE Q 53 TRP 0.017 0.001 TRP D 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (33520) covalent geometry : angle 0.42893 / 0.24 (45284) hydrogen bonds : bond 0.05199 / 3.46 ( 2573) hydrogen bonds : angle 3.11538 / 2.23 ( 7701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 416 time to evaluate : 1.383 Fit side-chains REVERT: A 141 LYS cc_start: 0.8188 (tttt) cc_final: 0.7868 (tmmt) REVERT: B 107 ASN cc_start: 0.9015 (t0) cc_final: 0.8781 (m-40) REVERT: B 125 ASP cc_start: 0.8438 (t0) cc_final: 0.7819 (t70) REVERT: C 34 TYR cc_start: 0.8513 (m-10) cc_final: 0.8266 (m-10) REVERT: D 68 TYR cc_start: 0.8880 (m-10) cc_final: 0.8569 (m-10) REVERT: F 67 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7819 (tm-30) REVERT: F 125 ASP cc_start: 0.8157 (t0) cc_final: 0.7590 (t0) REVERT: G 59 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7576 (mt-10) REVERT: G 67 GLU cc_start: 0.7492 (tp30) cc_final: 0.7286 (mm-30) REVERT: I 78 MET cc_start: 0.8376 (mtt) cc_final: 0.7994 (mtt) REVERT: I 81 LYS cc_start: 0.8026 (mttt) cc_final: 0.7796 (mmtp) REVERT: I 110 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8097 (mmm-85) REVERT: I 164 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: J 106 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8526 (mm-30) REVERT: J 150 VAL cc_start: 0.7627 (t) cc_final: 0.7366 (t) REVERT: K 47 MET cc_start: 0.7818 (mmm) cc_final: 0.7549 (mmt) REVERT: K 56 HIS cc_start: 0.7414 (m-70) cc_final: 0.7022 (t70) REVERT: L 46 ASP cc_start: 0.8531 (m-30) cc_final: 0.8245 (m-30) REVERT: L 79 LYS cc_start: 0.8332 (mptt) cc_final: 0.7699 (ptpt) REVERT: M 56 HIS cc_start: 0.7510 (t-90) cc_final: 0.7228 (t-90) REVERT: M 123 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7288 (tm-30) REVERT: M 164 GLU cc_start: 0.6938 (tt0) cc_final: 0.6644 (tp30) REVERT: N 125 ASP cc_start: 0.8381 (t0) cc_final: 0.8040 (t0) REVERT: Q 78 MET cc_start: 0.7987 (mtt) cc_final: 0.7667 (mtt) REVERT: Q 148 ASP cc_start: 0.8295 (t0) cc_final: 0.7980 (t0) REVERT: Q 169 MET cc_start: 0.7846 (ttm) cc_final: 0.7324 (ttm) REVERT: R 89 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8364 (mmtm) REVERT: S 15 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (mttm) REVERT: S 47 MET cc_start: 0.7441 (mtt) cc_final: 0.6686 (mmt) REVERT: S 56 HIS cc_start: 0.7824 (m-70) cc_final: 0.7464 (t70) REVERT: S 148 ASP cc_start: 0.7763 (m-30) cc_final: 0.7333 (m-30) REVERT: T 125 ASP cc_start: 0.8210 (t70) cc_final: 0.7866 (t70) REVERT: V 67 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7565 (tm-30) REVERT: V 116 ILE cc_start: 0.8223 (mt) cc_final: 0.7941 (mm) REVERT: W 29 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7887 (mt-10) REVERT: W 47 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (mmt) REVERT: W 164 GLU cc_start: 0.7082 (tt0) cc_final: 0.6344 (mt-10) REVERT: X 56 HIS cc_start: 0.6989 (t-90) cc_final: 0.6523 (t-90) REVERT: X 148 ASP cc_start: 0.7665 (p0) cc_final: 0.7308 (p0) outliers start: 35 outliers final: 20 residues processed: 436 average time/residue: 0.6211 time to fit residues: 330.3177 Evaluate side-chains 366 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 343 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 341 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 304 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN E 76 ASN F 76 ASN Q 22 GLN ** T 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 ASN W 22 GLN W 154 ASN X 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103015 restraints weight = 338828.574| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 5.32 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33520 Z= 0.126 Angle : 0.447 8.102 45284 Z= 0.252 Chirality : 0.038 0.171 4909 Planarity : 0.003 0.043 5825 Dihedral : 3.516 14.644 4332 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.94 % Allowed : 16.35 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.13), residues: 3995 helix: 2.77 (0.09), residues: 3124 sheet: None (None), residues: 0 loop : -1.06 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 137 TYR 0.020 0.001 TYR H 68 PHE 0.013 0.001 PHE Q 53 TRP 0.010 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (33520) covalent geometry : angle 0.44718 / 0.25 (45284) hydrogen bonds : bond 0.05732 / 3.82 ( 2573) hydrogen bonds : angle 3.16004 / 2.26 ( 7701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 1.434 Fit side-chains REVERT: A 141 LYS cc_start: 0.8147 (tttt) cc_final: 0.7777 (tmmt) REVERT: B 107 ASN cc_start: 0.8985 (t0) cc_final: 0.8769 (m-40) REVERT: B 125 ASP cc_start: 0.8360 (t0) cc_final: 0.7744 (t70) REVERT: B 158 ASP cc_start: 0.8449 (t0) cc_final: 0.8226 (t0) REVERT: C 34 TYR cc_start: 0.8518 (m-10) cc_final: 0.8228 (m-10) REVERT: D 68 TYR cc_start: 0.8844 (m-10) cc_final: 0.8509 (m-10) REVERT: D 78 MET cc_start: 0.8304 (mtt) cc_final: 0.6984 (mtt) REVERT: F 67 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7870 (tm-30) REVERT: F 125 ASP cc_start: 0.8188 (t0) cc_final: 0.7576 (t0) REVERT: G 59 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7488 (mt-10) REVERT: I 78 MET cc_start: 0.8430 (mtt) cc_final: 0.8013 (mtt) REVERT: I 81 LYS cc_start: 0.8008 (mttt) cc_final: 0.7733 (mmtp) REVERT: I 110 ARG cc_start: 0.8311 (mtp180) cc_final: 0.8085 (mmm-85) REVERT: I 164 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: J 106 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8620 (mm-30) REVERT: J 150 VAL cc_start: 0.7683 (t) cc_final: 0.7393 (t) REVERT: K 56 HIS cc_start: 0.7424 (m-70) cc_final: 0.6979 (t70) REVERT: L 46 ASP cc_start: 0.8479 (m-30) cc_final: 0.8192 (m-30) REVERT: L 67 GLU cc_start: 0.7547 (tt0) cc_final: 0.7235 (tm-30) REVERT: L 79 LYS cc_start: 0.8319 (mptt) cc_final: 0.7677 (ptpt) REVERT: M 56 HIS cc_start: 0.7496 (t-90) cc_final: 0.7206 (t-90) REVERT: M 123 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7316 (tm-30) REVERT: M 164 GLU cc_start: 0.6897 (tt0) cc_final: 0.6647 (tp30) REVERT: N 125 ASP cc_start: 0.8396 (t0) cc_final: 0.7959 (t0) REVERT: O 47 MET cc_start: 0.8195 (tpp) cc_final: 0.7902 (tpp) REVERT: O 105 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7317 (mmp80) REVERT: Q 78 MET cc_start: 0.7982 (mtt) cc_final: 0.7665 (mtt) REVERT: Q 148 ASP cc_start: 0.8276 (t0) cc_final: 0.7942 (t0) REVERT: Q 169 MET cc_start: 0.7881 (ttm) cc_final: 0.7358 (ttm) REVERT: R 89 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8402 (mmtm) REVERT: S 15 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7362 (mmtt) REVERT: S 47 MET cc_start: 0.7650 (mtt) cc_final: 0.6712 (mmt) REVERT: S 56 HIS cc_start: 0.7772 (m-70) cc_final: 0.7326 (t70) REVERT: S 148 ASP cc_start: 0.7740 (m-30) cc_final: 0.7304 (m-30) REVERT: T 125 ASP cc_start: 0.8209 (t70) cc_final: 0.7778 (t70) REVERT: V 67 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7538 (tm-30) REVERT: V 116 ILE cc_start: 0.8208 (mt) cc_final: 0.7909 (mm) REVERT: W 29 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7852 (mt-10) REVERT: W 47 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (mmt) REVERT: W 164 GLU cc_start: 0.7073 (tt0) cc_final: 0.6329 (mt-10) REVERT: X 56 HIS cc_start: 0.7034 (t-90) cc_final: 0.6484 (t-90) outliers start: 36 outliers final: 23 residues processed: 381 average time/residue: 0.6244 time to fit residues: 288.1572 Evaluate side-chains 370 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 344 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain P residue 43 ASP Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 200 optimal weight: 6.9990 chunk 375 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN H 17 ASN N 154 ASN P 76 ASN Q 22 GLN T 112 HIS V 14 ASN W 22 GLN W 154 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096813 restraints weight = 338552.677| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 5.16 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33520 Z= 0.182 Angle : 0.509 7.814 45284 Z= 0.288 Chirality : 0.040 0.181 4909 Planarity : 0.003 0.043 5825 Dihedral : 3.657 15.333 4332 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.85 % Allowed : 16.58 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.13), residues: 3995 helix: 2.50 (0.09), residues: 3148 sheet: None (None), residues: 0 loop : -1.37 (0.17), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 137 TYR 0.019 0.002 TYR A 24 PHE 0.017 0.001 PHE Q 53 TRP 0.012 0.001 TRP E 134 HIS 0.008 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (33520) covalent geometry : angle 0.50912 / 0.29 (45284) hydrogen bonds : bond 0.07786 / 5.20 ( 2573) hydrogen bonds : angle 3.52052 / 2.52 ( 7701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 1.381 Fit side-chains REVERT: A 141 LYS cc_start: 0.8239 (tttt) cc_final: 0.7905 (tmmt) REVERT: B 107 ASN cc_start: 0.9075 (t0) cc_final: 0.8848 (m-40) REVERT: B 125 ASP cc_start: 0.8493 (t0) cc_final: 0.7750 (t70) REVERT: E 172 LYS cc_start: 0.7554 (tptt) cc_final: 0.6662 (tppt) REVERT: F 67 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7986 (tm-30) REVERT: F 125 ASP cc_start: 0.8252 (t0) cc_final: 0.7679 (t70) REVERT: G 59 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7546 (mt-10) REVERT: H 68 TYR cc_start: 0.8653 (m-80) cc_final: 0.8371 (m-80) REVERT: I 22 GLN cc_start: 0.7630 (mm110) cc_final: 0.7291 (mt0) REVERT: I 81 LYS cc_start: 0.8072 (mttt) cc_final: 0.7866 (mmtp) REVERT: I 164 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6151 (tt0) REVERT: K 47 MET cc_start: 0.8063 (mmt) cc_final: 0.7833 (mmt) REVERT: K 56 HIS cc_start: 0.7599 (m-70) cc_final: 0.7148 (t70) REVERT: L 46 ASP cc_start: 0.8545 (m-30) cc_final: 0.8204 (m-30) REVERT: L 67 GLU cc_start: 0.7480 (tt0) cc_final: 0.7275 (tm-30) REVERT: L 79 LYS cc_start: 0.8372 (mptt) cc_final: 0.7738 (ptpt) REVERT: M 101 GLU cc_start: 0.7380 (tp30) cc_final: 0.7127 (mm-30) REVERT: M 123 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7402 (tm-30) REVERT: M 164 GLU cc_start: 0.6867 (tt0) cc_final: 0.6653 (tp30) REVERT: N 125 ASP cc_start: 0.8633 (t0) cc_final: 0.8320 (t0) REVERT: O 105 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7420 (mmp80) REVERT: Q 78 MET cc_start: 0.8305 (mtt) cc_final: 0.8005 (mtt) REVERT: Q 148 ASP cc_start: 0.8255 (t0) cc_final: 0.7964 (t0) REVERT: R 89 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8440 (mmtm) REVERT: S 15 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (mmtt) REVERT: S 47 MET cc_start: 0.8019 (mtt) cc_final: 0.7009 (mmt) REVERT: S 56 HIS cc_start: 0.7943 (m-70) cc_final: 0.7524 (t70) REVERT: S 148 ASP cc_start: 0.7977 (m-30) cc_final: 0.7544 (m-30) REVERT: T 125 ASP cc_start: 0.8520 (t70) cc_final: 0.8232 (t70) REVERT: V 67 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7616 (tm-30) REVERT: W 164 GLU cc_start: 0.7071 (tt0) cc_final: 0.6308 (mt-10) REVERT: X 56 HIS cc_start: 0.7166 (t-90) cc_final: 0.6637 (t-90) outliers start: 33 outliers final: 27 residues processed: 364 average time/residue: 0.6326 time to fit residues: 277.9048 Evaluate side-chains 362 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 165 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 154 ASN Q 22 GLN Q 56 HIS W 22 GLN W 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100621 restraints weight = 342993.394| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 5.32 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33520 Z= 0.137 Angle : 0.465 7.814 45284 Z= 0.264 Chirality : 0.038 0.175 4909 Planarity : 0.003 0.041 5825 Dihedral : 3.605 15.198 4332 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.82 % Allowed : 16.83 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.13), residues: 3995 helix: 2.71 (0.09), residues: 3124 sheet: None (None), residues: 0 loop : -1.01 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 137 TYR 0.020 0.001 TYR R 103 PHE 0.015 0.001 PHE Q 53 TRP 0.011 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (33520) covalent geometry : angle 0.46478 / 0.26 (45284) hydrogen bonds : bond 0.06368 / 4.25 ( 2573) hydrogen bonds : angle 3.29676 / 2.36 ( 7701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 1.412 Fit side-chains REVERT: A 141 LYS cc_start: 0.8246 (tttt) cc_final: 0.7885 (tmmt) REVERT: B 107 ASN cc_start: 0.9035 (t0) cc_final: 0.8814 (m-40) REVERT: B 125 ASP cc_start: 0.8441 (t0) cc_final: 0.7688 (t70) REVERT: C 34 TYR cc_start: 0.8552 (m-10) cc_final: 0.8292 (m-10) REVERT: C 55 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7910 (tp40) REVERT: D 68 TYR cc_start: 0.8913 (m-10) cc_final: 0.8574 (m-10) REVERT: F 67 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7923 (tm-30) REVERT: F 125 ASP cc_start: 0.8264 (t0) cc_final: 0.7667 (t0) REVERT: G 59 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7523 (mt-10) REVERT: H 68 TYR cc_start: 0.8681 (m-80) cc_final: 0.8468 (m-80) REVERT: I 22 GLN cc_start: 0.7577 (mm110) cc_final: 0.7228 (mt0) REVERT: I 78 MET cc_start: 0.8549 (mtt) cc_final: 0.8121 (mtt) REVERT: I 81 LYS cc_start: 0.8074 (mttt) cc_final: 0.7837 (mmtp) REVERT: I 110 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8136 (mmm-85) REVERT: I 164 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6011 (tt0) REVERT: K 56 HIS cc_start: 0.7515 (m-70) cc_final: 0.7097 (t70) REVERT: L 46 ASP cc_start: 0.8584 (m-30) cc_final: 0.8273 (m-30) REVERT: L 67 GLU cc_start: 0.7493 (tt0) cc_final: 0.7229 (tm-30) REVERT: L 79 LYS cc_start: 0.8382 (mptt) cc_final: 0.7754 (ptpt) REVERT: M 56 HIS cc_start: 0.7538 (t-90) cc_final: 0.7244 (t-90) REVERT: M 123 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7320 (tm-30) REVERT: M 164 GLU cc_start: 0.6893 (tt0) cc_final: 0.6685 (tp30) REVERT: N 125 ASP cc_start: 0.8500 (t0) cc_final: 0.8153 (t0) REVERT: O 105 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7277 (mmp80) REVERT: Q 67 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7412 (tt0) REVERT: Q 78 MET cc_start: 0.8172 (mtt) cc_final: 0.7851 (mtt) REVERT: Q 148 ASP cc_start: 0.8210 (t0) cc_final: 0.7928 (t0) REVERT: Q 169 MET cc_start: 0.7910 (ttm) cc_final: 0.7429 (ttm) REVERT: R 89 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8434 (mmtm) REVERT: S 15 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7662 (mmtt) REVERT: S 47 MET cc_start: 0.7734 (mtt) cc_final: 0.6806 (mmt) REVERT: S 56 HIS cc_start: 0.7818 (m-70) cc_final: 0.7392 (t70) REVERT: S 148 ASP cc_start: 0.7856 (m-30) cc_final: 0.7417 (m-30) REVERT: S 164 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: T 125 ASP cc_start: 0.8423 (t70) cc_final: 0.8076 (t70) REVERT: V 67 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7586 (tm-30) REVERT: V 116 ILE cc_start: 0.8386 (mt) cc_final: 0.8064 (mm) REVERT: W 164 GLU cc_start: 0.7113 (tt0) cc_final: 0.6263 (mt-10) REVERT: X 56 HIS cc_start: 0.7089 (t-90) cc_final: 0.6567 (t-90) outliers start: 32 outliers final: 24 residues processed: 360 average time/residue: 0.6227 time to fit residues: 272.3059 Evaluate side-chains 361 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 317 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN Q 22 GLN Q 56 HIS V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098886 restraints weight = 340104.626| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.28 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33520 Z= 0.157 Angle : 0.481 7.831 45284 Z= 0.272 Chirality : 0.039 0.177 4909 Planarity : 0.003 0.043 5825 Dihedral : 3.620 15.114 4332 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.82 % Allowed : 16.97 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.13), residues: 3995 helix: 2.59 (0.09), residues: 3148 sheet: None (None), residues: 0 loop : -1.26 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 137 TYR 0.019 0.001 TYR R 103 PHE 0.017 0.001 PHE Q 53 TRP 0.011 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (33520) covalent geometry : angle 0.48061 / 0.27 (45284) hydrogen bonds : bond 0.06939 / 4.63 ( 2573) hydrogen bonds : angle 3.37749 / 2.41 ( 7701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8077.23 seconds wall clock time: 139 minutes 4.85 seconds (8344.85 seconds total)