Starting phenix.real_space_refine on Mon Jul 6 03:36:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.map" model { file = "/net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr0_37759/07_2026/8wr0_37759.cif" } resolution = 3.1 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= 0.109 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 20993 2.51 5 N 5344 2.21 5 O 6408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 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: 32841 Number of models: 1 Model: "" Number of chains: 48 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: 1355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 3 bond proxies already assigned to first conformer: 1342 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: "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: "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: "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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 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: "X" 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 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: 13.55, per 1000 atoms: 0.41 Number of scatterers: 32841 At special positions: 0 Unit cell: (140.285, 136.097, 136.097, 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 6408 8.00 N 5344 7.00 C 20993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 2.5 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 12 sheets defined 82.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 14 through 45 Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.569A pdb=" N LYS A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.500A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 123 removed outlier: 3.784A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 4.405A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.694A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 44 Processing helix chain 'B' and resid 47 through 62 Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.742A pdb=" N SER B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 122 removed outlier: 3.731A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.705A pdb=" N PHE B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.172A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 44 Processing helix chain 'C' and resid 47 through 62 Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.669A pdb=" N GLU C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 123 removed outlier: 3.920A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 4.714A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.574A pdb=" N ILE C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 46 removed outlier: 3.795A pdb=" N ASP D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 63 through 77 removed outlier: 3.562A pdb=" N GLU D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 122 Processing helix chain 'D' and resid 125 through 151 removed outlier: 4.534A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.558A pdb=" N ILE D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 44 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.596A pdb=" N GLU E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.735A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 132 Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.959A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 156 removed outlier: 3.514A pdb=" N PHE E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN E 154 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER E 156 " --> pdb=" O PHE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 171 removed outlier: 3.721A pdb=" N ILE E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 44 Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.405A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.607A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 3.764A pdb=" N PHE F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.841A pdb=" N SER F 156 " --> pdb=" O PHE F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'G' and resid 14 through 44 Processing helix chain 'G' and resid 47 through 62 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.645A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 123 removed outlier: 3.845A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 4.456A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 158 through 172 removed outlier: 3.996A pdb=" N ILE G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 45 removed outlier: 3.610A pdb=" N PHE H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.255A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 122 removed outlier: 3.510A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 151 removed outlier: 4.580A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.949A 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 62 Processing helix chain 'I' and resid 63 through 77 removed outlier: 3.674A pdb=" N GLU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 122 removed outlier: 3.600A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 3.540A pdb=" N PHE I 129 " --> pdb=" O ASP I 125 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 171 removed outlier: 3.568A pdb=" N ILE I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 45 removed outlier: 3.528A pdb=" N PHE J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 62 removed outlier: 3.595A pdb=" N GLY J 51 " --> pdb=" O MET J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.952A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 122 removed outlier: 3.608A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 151 removed outlier: 4.614A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 171 removed outlier: 3.834A pdb=" N ILE J 162 " --> pdb=" O ASP J 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 171 " --> pdb=" O LYS J 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 44 Processing helix chain 'K' and resid 47 through 62 Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.675A pdb=" N GLU K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.840A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 151 removed outlier: 4.527A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 171 removed outlier: 3.724A pdb=" N ILE K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 46 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.449A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 123 removed outlier: 3.731A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 151 removed outlier: 3.765A pdb=" N PHE M 129 " --> pdb=" O ASP M 125 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP M 134 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU M 145 " --> pdb=" O LYS M 141 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL M 146 " --> pdb=" O ASP M 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 171 removed outlier: 3.513A pdb=" N ILE M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU M 171 " --> pdb=" O LYS M 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 44 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 63 through 77 removed outlier: 3.684A pdb=" N GLU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 122 removed outlier: 3.546A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 4.649A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.594A 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 removed outlier: 3.524A pdb=" N VAL N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 44 Processing helix chain 'O' and resid 47 through 62 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.530A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY O 77 " --> pdb=" O PHE O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 123 removed outlier: 3.735A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 3.710A pdb=" N PHE O 129 " --> pdb=" O ASP O 125 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 removed outlier: 3.611A pdb=" N ILE O 162 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 44 Processing helix chain 'P' and resid 47 through 62 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.431A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.899A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 4.549A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 171 removed outlier: 3.709A pdb=" N ILE P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU P 171 " --> pdb=" O LYS P 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 46 removed outlier: 3.810A pdb=" N ASP Q 46 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 62 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.460A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 123 removed outlier: 3.937A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 3.740A pdb=" N PHE Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 171 removed outlier: 3.636A pdb=" N ILE Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU Q 171 " --> pdb=" O LYS Q 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 45 removed outlier: 3.604A pdb=" N PHE R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 62 Processing helix chain 'R' and resid 63 through 77 removed outlier: 3.530A pdb=" N GLU R 67 " --> pdb=" O GLY R 63 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.630A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 3.647A pdb=" N PHE R 129 " --> pdb=" O ASP R 125 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.954A pdb=" N ILE R 162 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS R 172 " --> pdb=" O GLU R 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 45 Processing helix chain 'S' and resid 47 through 62 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.533A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.936A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 151 removed outlier: 4.699A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 156 removed outlier: 4.082A pdb=" N SER S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 171 removed outlier: 3.793A pdb=" N ILE S 162 " --> pdb=" O ASP S 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU S 171 " --> pdb=" O LYS S 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 44 Processing helix chain 'T' and resid 47 through 62 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.420A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.829A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 151 removed outlier: 3.508A pdb=" N ILE T 132 " --> pdb=" O SER T 128 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 171 removed outlier: 4.070A pdb=" N ILE T 162 " --> pdb=" O ASP T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 46 removed outlier: 3.508A pdb=" N PHE U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 62 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.733A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.985A pdb=" N ARG U 110 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 4.726A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 4.108A 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 removed outlier: 3.721A pdb=" N ILE U 162 " --> pdb=" O ASP U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 46 removed outlier: 3.634A pdb=" N ASP V 46 " --> pdb=" O ASP V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 62 Processing helix chain 'V' and resid 63 through 77 removed outlier: 3.548A pdb=" N GLU V 67 " --> pdb=" O GLY V 63 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 Processing helix chain 'V' and resid 125 through 151 removed outlier: 4.650A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 171 Processing helix chain 'W' and resid 14 through 44 Processing helix chain 'W' and resid 47 through 61 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.379A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 123 removed outlier: 3.805A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 4.689A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL W 146 " --> pdb=" O ASP W 142 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 156 removed outlier: 3.924A pdb=" N SER W 155 " --> pdb=" O LYS W 151 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER W 156 " --> pdb=" O LEU W 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 151 through 156' Processing helix chain 'W' and resid 158 through 171 removed outlier: 3.712A pdb=" N ILE W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU W 171 " --> pdb=" O LYS W 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 45 removed outlier: 3.782A pdb=" N PHE X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 62 Processing helix chain 'X' and resid 66 through 77 Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.808A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 3.693A pdb=" N PHE X 129 " --> pdb=" O ASP X 125 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 172 removed outlier: 3.720A pdb=" N ILE X 162 " --> pdb=" O ASP X 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 44 Processing helix chain 'L' and resid 47 through 62 Processing helix chain 'L' and resid 63 through 77 removed outlier: 3.530A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.781A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 151 removed outlier: 4.468A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 156 removed outlier: 3.711A pdb=" N SER L 155 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER L 156 " --> pdb=" O PHE L 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 152 through 156' Processing helix chain 'L' and resid 158 through 171 removed outlier: 3.767A pdb=" N ILE L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU L 171 " --> pdb=" O LYS L 167 " (cutoff:3.500A) 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 88 removed outlier: 4.874A pdb=" N THR G 82 " --> pdb=" O VAL B 88 " (cutoff:3.500A) 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 83 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 86 Processing sheet with id=AA7, first strand: chain 'K' and resid 84 through 86 removed outlier: 3.599A pdb=" N VAL W 86 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL K 86 " --> pdb=" O VAL W 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'O' and resid 83 through 87 removed outlier: 3.645A pdb=" N VAL S 84 " --> pdb=" O VAL O 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'Q' and resid 83 through 87 2517 hydrogen bonds defined for protein. 7539 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: 5.81 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7043 1.33 - 1.45: 7585 1.45 - 1.56: 18738 1.56 - 1.68: 0 1.68 - 1.80: 144 Bond restraints: 33510 Sorted by residual: bond pdb=" CA GLU W 178 " pdb=" C GLU W 178 " ideal model delta sigma weight residual 1.526 1.495 0.031 9.20e-03 1.18e+04 1.17e+01 bond pdb=" C ILE W 179 " pdb=" O ILE W 179 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.12e-02 7.97e+03 5.76e+00 bond pdb=" CA TRP W 180 " pdb=" C TRP W 180 " ideal model delta sigma weight residual 1.522 1.492 0.031 1.34e-02 5.57e+03 5.22e+00 bond pdb=" N ILE W 179 " pdb=" CA ILE W 179 " ideal model delta sigma weight residual 1.460 1.435 0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" N GLU W 178 " pdb=" CA GLU W 178 " ideal model delta sigma weight residual 1.468 1.444 0.025 1.24e-02 6.50e+03 3.90e+00 ... (remaining 33505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 44010 1.50 - 3.00: 1117 3.00 - 4.50: 124 4.50 - 6.00: 15 6.00 - 7.50: 3 Bond angle restraints: 45269 Sorted by residual: angle pdb=" N VAL D 149 " pdb=" CA VAL D 149 " pdb=" C VAL D 149 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.94e+01 angle pdb=" N VAL V 149 " pdb=" CA VAL V 149 " pdb=" C VAL V 149 " ideal model delta sigma weight residual 111.81 108.88 2.93 8.60e-01 1.35e+00 1.16e+01 angle pdb=" N TRP W 180 " pdb=" CA TRP W 180 " pdb=" C TRP W 180 " ideal model delta sigma weight residual 113.38 117.35 -3.97 1.23e+00 6.61e-01 1.04e+01 angle pdb=" N ILE W 179 " pdb=" CA ILE W 179 " pdb=" C ILE W 179 " ideal model delta sigma weight residual 110.53 113.56 -3.03 9.40e-01 1.13e+00 1.04e+01 angle pdb=" C THR C 144 " pdb=" N GLU C 145 " pdb=" CA GLU C 145 " ideal model delta sigma weight residual 122.38 116.80 5.58 1.81e+00 3.05e-01 9.52e+00 ... (remaining 45264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.37: 18550 20.37 - 40.74: 1313 40.74 - 61.11: 177 61.11 - 81.48: 61 81.48 - 101.85: 16 Dihedral angle restraints: 20117 sinusoidal: 8179 harmonic: 11938 Sorted by residual: dihedral pdb=" CB BGLU I 108 " pdb=" CG BGLU I 108 " pdb=" CD BGLU I 108 " pdb=" OE1BGLU I 108 " ideal model delta sinusoidal sigma weight residual 0.00 101.85 -101.85 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" CA GLU C 145 " pdb=" C GLU C 145 " pdb=" N VAL C 146 " pdb=" CA VAL C 146 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP T 138 " pdb=" CB ASP T 138 " pdb=" CG ASP T 138 " pdb=" OD1 ASP T 138 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 20114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3740 0.049 - 0.098: 1044 0.098 - 0.147: 122 0.147 - 0.195: 1 0.195 - 0.244: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" CA TRP W 180 " pdb=" N TRP W 180 " pdb=" C TRP W 180 " pdb=" CB TRP W 180 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ILE W 179 " pdb=" N ILE W 179 " pdb=" C ILE W 179 " pdb=" CB ILE W 179 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ASP P 46 " pdb=" N ASP P 46 " pdb=" C ASP P 46 " pdb=" CB ASP P 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 4905 not shown) Planarity restraints: 5822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE J 91 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO J 92 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 92 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET I 47 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO I 48 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 48 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 48 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 91 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO L 92 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 92 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 92 " 0.023 5.00e-02 4.00e+02 ... (remaining 5819 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 153 2.52 - 3.11: 24052 3.11 - 3.71: 48866 3.71 - 4.30: 68115 4.30 - 4.90: 116704 Nonbonded interactions: 257890 Sorted by model distance: nonbonded pdb=" OD2 ASP A 138 " pdb="FE FE A 201 " model vdw 1.919 3.000 nonbonded pdb=" OD2 ASP W 138 " pdb="FE FE W 201 " model vdw 1.922 3.000 nonbonded pdb=" OD2 ASP I 138 " pdb="FE FE I 201 " model vdw 1.936 3.000 nonbonded pdb=" OD2 ASP H 138 " pdb="FE FE H 201 " model vdw 1.941 3.000 nonbonded pdb=" OD2 ASP F 138 " pdb="FE FE F 201 " model vdw 1.942 3.000 ... (remaining 257885 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 \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 176 or resid 178 through 201) \ ) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 132 or resid 134 through 147 or resid 149 through 171 or resid 178 through 201) \ ) } 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: 1.470 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.970 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.038 33510 Z= 0.255 Angle : 0.578 7.499 45269 Z= 0.342 Chirality : 0.042 0.244 4908 Planarity : 0.003 0.048 5822 Dihedral : 14.386 101.846 12413 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.81 % Allowed : 2.83 % Favored : 96.35 % 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: -1.40 (0.11), residues: 3992 helix: -0.29 (0.08), residues: 3064 sheet: None (None), residues: 0 loop : -2.80 (0.14), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 110 TYR 0.020 0.002 TYR K 24 PHE 0.016 0.002 PHE N 131 TRP 0.008 0.001 TRP G 134 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (33510) covalent geometry : angle 0.57787 / 0.34 (45269) hydrogen bonds : bond 0.13919 / 9.39 ( 2517) hydrogen bonds : angle 5.00836 / 3.57 ( 7539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 582 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASP cc_start: 0.8070 (t70) cc_final: 0.7656 (t0) REVERT: B 78 MET cc_start: 0.9097 (mtt) cc_final: 0.8437 (mtt) REVERT: B 81 LYS cc_start: 0.7297 (mttt) cc_final: 0.7057 (mtpp) REVERT: B 106 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 141 LYS cc_start: 0.6733 (tttt) cc_final: 0.6473 (tmmt) REVERT: B 167 LYS cc_start: 0.7700 (tttm) cc_final: 0.7485 (tttt) REVERT: C 105 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7176 (mmp80) REVERT: D 148 ASP cc_start: 0.8383 (t0) cc_final: 0.7997 (t0) REVERT: E 15 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8001 (mttp) REVERT: F 106 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8337 (mm-30) REVERT: G 78 MET cc_start: 0.8430 (mtt) cc_final: 0.8136 (mtt) REVERT: G 137 ARG cc_start: 0.7846 (tmm160) cc_final: 0.7640 (ttp80) REVERT: H 55 GLN cc_start: 0.8056 (tp40) cc_final: 0.7757 (tp-100) REVERT: I 56 HIS cc_start: 0.7613 (m-70) cc_final: 0.7264 (t-90) REVERT: I 83 ASP cc_start: 0.8131 (t0) cc_final: 0.7918 (m-30) REVERT: I 124 ASP cc_start: 0.8265 (m-30) cc_final: 0.7694 (t0) REVERT: J 81 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7737 (mtmm) REVERT: K 16 ILE cc_start: 0.8324 (mm) cc_final: 0.7885 (mm) REVERT: M 55 GLN cc_start: 0.7931 (tp40) cc_final: 0.7608 (tp40) REVERT: M 167 LYS cc_start: 0.8488 (tttm) cc_final: 0.8050 (ttpp) REVERT: O 105 ARG cc_start: 0.7241 (mmt90) cc_final: 0.6725 (mmp-170) REVERT: Q 78 MET cc_start: 0.7666 (mtt) cc_final: 0.7233 (mtt) REVERT: T 22 GLN cc_start: 0.7643 (tp40) cc_final: 0.7102 (tm-30) REVERT: T 26 LEU cc_start: 0.6654 (pp) cc_final: 0.6322 (mt) REVERT: U 59 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7536 (mt-10) REVERT: U 78 MET cc_start: 0.6927 (mtt) cc_final: 0.6643 (mtt) REVERT: U 85 SER cc_start: 0.8864 (p) cc_final: 0.8649 (m) REVERT: V 29 GLU cc_start: 0.8015 (pt0) cc_final: 0.7724 (pt0) REVERT: V 101 GLU cc_start: 0.7921 (tp30) cc_final: 0.7585 (tp30) REVERT: W 147 ASP cc_start: 0.8245 (t70) cc_final: 0.7797 (t0) REVERT: W 151 LYS cc_start: 0.8354 (pttp) cc_final: 0.8038 (ptmt) REVERT: W 167 LYS cc_start: 0.7578 (tttm) cc_final: 0.7241 (ttpt) REVERT: X 89 LYS cc_start: 0.9099 (ptpt) cc_final: 0.8826 (ptpp) REVERT: X 137 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7766 (ttm170) outliers start: 1 outliers final: 1 residues processed: 583 average time/residue: 0.2109 time to fit residues: 196.9482 Evaluate side-chains 430 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 179 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 21 ASN A 27 ASN A 154 ASN B 17 ASN B 154 ASN E 17 ASN E 22 GLN E 154 ASN F 17 ASN G 22 GLN G 55 GLN H 100 GLN H 112 HIS H 157 ASN J 17 ASN K 39 HIS M 39 HIS N 22 GLN N 154 ASN O 17 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN S 21 ASN S 36 HIS U 154 ASN V 17 ASN W 17 ASN W 65 HIS W 76 ASN X 17 ASN X 22 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099784 restraints weight = 347537.290| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 5.81 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33510 Z= 0.146 Angle : 0.488 7.498 45269 Z= 0.277 Chirality : 0.039 0.166 4908 Planarity : 0.003 0.042 5822 Dihedral : 3.873 14.708 4332 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.54 % Allowed : 7.32 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 3992 helix: 1.19 (0.09), residues: 3133 sheet: None (None), residues: 0 loop : -2.19 (0.15), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 137 TYR 0.017 0.001 TYR K 24 PHE 0.014 0.001 PHE S 131 TRP 0.007 0.001 TRP K 180 HIS 0.009 0.001 HIS F 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (33510) covalent geometry : angle 0.48762 / 0.28 (45269) hydrogen bonds : bond 0.06941 / 4.65 ( 2517) hydrogen bonds : angle 3.66247 / 2.62 ( 7539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 523 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8756 (m-10) cc_final: 0.8507 (m-80) REVERT: B 76 ASN cc_start: 0.8209 (p0) cc_final: 0.7701 (p0) REVERT: B 78 MET cc_start: 0.8975 (mtt) cc_final: 0.8600 (mtt) REVERT: B 141 LYS cc_start: 0.7333 (tttt) cc_final: 0.7126 (tmmt) REVERT: B 167 LYS cc_start: 0.8385 (tttm) cc_final: 0.8147 (tttt) REVERT: B 169 MET cc_start: 0.8530 (ttm) cc_final: 0.8273 (mtp) REVERT: C 105 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7525 (mmp80) REVERT: D 148 ASP cc_start: 0.8332 (t0) cc_final: 0.7995 (t0) REVERT: D 169 MET cc_start: 0.8806 (ttm) cc_final: 0.8384 (ttm) REVERT: G 147 ASP cc_start: 0.8723 (t70) cc_final: 0.8441 (t70) REVERT: I 22 GLN cc_start: 0.7884 (tt0) cc_final: 0.7545 (mt0) REVERT: I 124 ASP cc_start: 0.8339 (m-30) cc_final: 0.8118 (t0) REVERT: K 16 ILE cc_start: 0.8354 (mm) cc_final: 0.7753 (mm) REVERT: K 105 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7984 (mmt90) REVERT: K 151 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7655 (mtmt) REVERT: M 167 LYS cc_start: 0.9014 (tttm) cc_final: 0.8799 (tttm) REVERT: N 103 TYR cc_start: 0.8523 (t80) cc_final: 0.8323 (t80) REVERT: O 67 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7349 (tm-30) REVERT: O 105 ARG cc_start: 0.7662 (mmt90) cc_final: 0.7420 (mmp-170) REVERT: O 148 ASP cc_start: 0.8572 (m-30) cc_final: 0.8289 (m-30) REVERT: Q 25 LYS cc_start: 0.8112 (tttp) cc_final: 0.7747 (tttt) REVERT: Q 79 LYS cc_start: 0.7369 (pttm) cc_final: 0.7162 (mtpt) REVERT: R 42 ASP cc_start: 0.8528 (t0) cc_final: 0.8258 (t0) REVERT: S 55 GLN cc_start: 0.7983 (tp40) cc_final: 0.7676 (tp-100) REVERT: V 56 HIS cc_start: 0.7764 (t70) cc_final: 0.7464 (t70) REVERT: W 147 ASP cc_start: 0.8647 (t70) cc_final: 0.8213 (t0) REVERT: W 167 LYS cc_start: 0.7996 (tttm) cc_final: 0.7731 (ttpt) REVERT: X 91 ILE cc_start: 0.9197 (mp) cc_final: 0.8993 (mp) REVERT: L 78 MET cc_start: 0.8482 (mtt) cc_final: 0.8099 (mtt) outliers start: 25 outliers final: 17 residues processed: 536 average time/residue: 0.2003 time to fit residues: 173.6539 Evaluate side-chains 451 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 434 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain U residue 56 HIS Chi-restraints excluded: chain W residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 225 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN C 76 ASN E 17 ASN E 22 GLN F 76 ASN H 157 ASN J 17 ASN J 23 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN R 56 HIS T 76 ASN U 76 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 76 ASN L 39 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093977 restraints weight = 331587.409| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 5.62 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 33510 Z= 0.217 Angle : 0.540 6.693 45269 Z= 0.305 Chirality : 0.041 0.186 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.891 14.967 4330 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.24 % Allowed : 9.82 % Favored : 87.93 % 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: 1.02 (0.13), residues: 3992 helix: 1.41 (0.09), residues: 3133 sheet: None (None), residues: 0 loop : -2.05 (0.16), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 137 TYR 0.019 0.002 TYR K 24 PHE 0.015 0.001 PHE N 131 TRP 0.007 0.001 TRP T 134 HIS 0.006 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (33510) covalent geometry : angle 0.54021 / 0.31 (45269) hydrogen bonds : bond 0.08383 / 5.62 ( 2517) hydrogen bonds : angle 3.88218 / 2.78 ( 7539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 431 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 76 ASN cc_start: 0.8322 (p0) cc_final: 0.8046 (p0) REVERT: B 78 MET cc_start: 0.9026 (mtt) cc_final: 0.8658 (mtt) REVERT: B 141 LYS cc_start: 0.7460 (tttt) cc_final: 0.7219 (tmmt) REVERT: B 167 LYS cc_start: 0.8365 (tttm) cc_final: 0.8128 (tttt) REVERT: C 78 MET cc_start: 0.8459 (mtt) cc_final: 0.7856 (mtt) REVERT: C 105 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7625 (mmp80) REVERT: I 22 GLN cc_start: 0.7895 (tt0) cc_final: 0.7530 (mt0) REVERT: I 124 ASP cc_start: 0.8374 (m-30) cc_final: 0.8161 (t0) REVERT: K 16 ILE cc_start: 0.8483 (mm) cc_final: 0.7850 (mm) REVERT: K 105 ARG cc_start: 0.8265 (mmt90) cc_final: 0.8035 (mmt90) REVERT: K 151 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7718 (mtmt) REVERT: M 124 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8448 (t0) REVERT: M 167 LYS cc_start: 0.9034 (tttm) cc_final: 0.8794 (tttm) REVERT: O 105 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7454 (mmp-170) REVERT: O 148 ASP cc_start: 0.8517 (m-30) cc_final: 0.8226 (m-30) REVERT: P 47 MET cc_start: 0.9033 (mtp) cc_final: 0.8790 (mtp) REVERT: Q 49 TYR cc_start: 0.8659 (m-80) cc_final: 0.8348 (m-80) REVERT: Q 79 LYS cc_start: 0.7450 (pttm) cc_final: 0.7087 (mtpt) REVERT: Q 100 GLN cc_start: 0.7859 (mt0) cc_final: 0.7596 (mt0) REVERT: R 42 ASP cc_start: 0.8583 (t0) cc_final: 0.8300 (t0) REVERT: W 167 LYS cc_start: 0.7988 (tttm) cc_final: 0.7712 (ttpt) outliers start: 51 outliers final: 39 residues processed: 458 average time/residue: 0.2021 time to fit residues: 149.9777 Evaluate side-chains 444 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 404 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain U residue 85 SER Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 322 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN C 76 ASN E 22 GLN H 157 ASN M 17 ASN M 56 HIS ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN U 76 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099725 restraints weight = 322403.590| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.60 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33510 Z= 0.138 Angle : 0.457 6.214 45269 Z= 0.260 Chirality : 0.038 0.174 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.722 13.917 4330 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.77 % Allowed : 11.34 % Favored : 86.90 % 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: 1.76 (0.13), residues: 3992 helix: 1.92 (0.09), residues: 3129 sheet: None (None), residues: 0 loop : -1.75 (0.16), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 75 TYR 0.022 0.001 TYR N 103 PHE 0.012 0.001 PHE S 131 TRP 0.006 0.001 TRP Q 134 HIS 0.007 0.001 HIS I 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (33510) covalent geometry : angle 0.45722 / 0.26 (45269) hydrogen bonds : bond 0.06453 / 4.32 ( 2517) hydrogen bonds : angle 3.44868 / 2.47 ( 7539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 453 time to evaluate : 1.056 Fit side-chains REVERT: B 78 MET cc_start: 0.8908 (mtt) cc_final: 0.8590 (mtt) REVERT: B 141 LYS cc_start: 0.7357 (tttt) cc_final: 0.7135 (tmmt) REVERT: B 167 LYS cc_start: 0.8385 (tttm) cc_final: 0.8135 (tttt) REVERT: B 169 MET cc_start: 0.8486 (ttm) cc_final: 0.8254 (mtp) REVERT: C 22 GLN cc_start: 0.8149 (tt0) cc_final: 0.7826 (mt0) REVERT: C 105 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7465 (mmp80) REVERT: G 147 ASP cc_start: 0.8795 (t70) cc_final: 0.8533 (t0) REVERT: I 22 GLN cc_start: 0.7800 (tt0) cc_final: 0.7509 (mt0) REVERT: J 59 GLU cc_start: 0.8194 (tp30) cc_final: 0.7927 (mt-10) REVERT: K 16 ILE cc_start: 0.8339 (mm) cc_final: 0.7727 (mm) REVERT: K 151 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7544 (mtmt) REVERT: M 151 LYS cc_start: 0.8598 (ptpt) cc_final: 0.7945 (ptpp) REVERT: M 167 LYS cc_start: 0.9013 (tttm) cc_final: 0.8791 (tttm) REVERT: O 105 ARG cc_start: 0.7678 (mmt90) cc_final: 0.7382 (mmp-170) REVERT: O 148 ASP cc_start: 0.8500 (m-30) cc_final: 0.8165 (m-30) REVERT: Q 79 LYS cc_start: 0.7522 (pttm) cc_final: 0.7126 (mtpt) REVERT: R 42 ASP cc_start: 0.8458 (t0) cc_final: 0.8191 (t0) REVERT: T 22 GLN cc_start: 0.7790 (tp40) cc_final: 0.7500 (tm-30) REVERT: V 56 HIS cc_start: 0.7861 (t70) cc_final: 0.7637 (t70) REVERT: V 106 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8404 (mm-30) REVERT: W 167 LYS cc_start: 0.7968 (tttm) cc_final: 0.7707 (ttpt) REVERT: L 78 MET cc_start: 0.8384 (mtt) cc_final: 0.8048 (mtt) outliers start: 33 outliers final: 26 residues processed: 471 average time/residue: 0.2085 time to fit residues: 158.6353 Evaluate side-chains 447 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 421 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 302 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 320 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN B 22 GLN E 22 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN U 76 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101233 restraints weight = 365722.838| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.96 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33510 Z= 0.124 Angle : 0.438 7.007 45269 Z= 0.250 Chirality : 0.038 0.189 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.616 13.890 4330 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.80 % Allowed : 11.95 % Favored : 86.25 % 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: 2.20 (0.13), residues: 3992 helix: 2.22 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.52 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 75 TYR 0.019 0.001 TYR N 103 PHE 0.010 0.001 PHE S 131 TRP 0.005 0.001 TRP Q 134 HIS 0.006 0.001 HIS I 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (33510) covalent geometry : angle 0.43789 / 0.25 (45269) hydrogen bonds : bond 0.05880 / 3.94 ( 2517) hydrogen bonds : angle 3.27892 / 2.35 ( 7539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 450 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: B 78 MET cc_start: 0.8903 (mtt) cc_final: 0.8478 (mtt) REVERT: B 167 LYS cc_start: 0.8399 (tttm) cc_final: 0.8149 (tttt) REVERT: C 22 GLN cc_start: 0.8107 (tt0) cc_final: 0.7812 (mt0) REVERT: C 105 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7443 (mmp80) REVERT: G 147 ASP cc_start: 0.8762 (t70) cc_final: 0.8492 (t0) REVERT: J 59 GLU cc_start: 0.8175 (tp30) cc_final: 0.7924 (mt-10) REVERT: J 85 SER cc_start: 0.8973 (t) cc_final: 0.8141 (m) REVERT: J 169 MET cc_start: 0.7918 (ttm) cc_final: 0.7696 (ttm) REVERT: K 16 ILE cc_start: 0.8189 (mm) cc_final: 0.7602 (mm) REVERT: K 151 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7492 (mtmt) REVERT: M 167 LYS cc_start: 0.8997 (tttm) cc_final: 0.8769 (tttm) REVERT: O 105 ARG cc_start: 0.7619 (mmt90) cc_final: 0.7273 (mmp-170) REVERT: O 148 ASP cc_start: 0.8469 (m-30) cc_final: 0.8122 (m-30) REVERT: Q 79 LYS cc_start: 0.7560 (pttm) cc_final: 0.7142 (mtpt) REVERT: Q 158 ASP cc_start: 0.7618 (m-30) cc_final: 0.7194 (m-30) REVERT: R 42 ASP cc_start: 0.8417 (t0) cc_final: 0.8164 (t0) REVERT: S 47 MET cc_start: 0.8609 (mmm) cc_final: 0.7775 (mmt) REVERT: V 56 HIS cc_start: 0.7828 (t70) cc_final: 0.7624 (t70) REVERT: V 106 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8288 (mm-30) REVERT: W 167 LYS cc_start: 0.8031 (tttm) cc_final: 0.7718 (ttpt) REVERT: L 78 MET cc_start: 0.8325 (mtt) cc_final: 0.8036 (mtt) outliers start: 33 outliers final: 28 residues processed: 463 average time/residue: 0.1941 time to fit residues: 146.2832 Evaluate side-chains 437 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 409 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 133 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN D 154 ASN E 22 GLN H 76 ASN H 157 ASN I 65 HIS ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS S 100 GLN U 76 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092830 restraints weight = 322724.143| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 5.56 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 33510 Z= 0.253 Angle : 0.573 7.093 45269 Z= 0.322 Chirality : 0.042 0.199 4908 Planarity : 0.004 0.048 5822 Dihedral : 3.889 15.540 4330 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.38 % Allowed : 12.18 % Favored : 85.44 % 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: 1.64 (0.12), residues: 3992 helix: 1.78 (0.09), residues: 3127 sheet: None (None), residues: 0 loop : -1.53 (0.17), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 137 TYR 0.022 0.002 TYR K 24 PHE 0.016 0.002 PHE N 131 TRP 0.008 0.001 TRP M 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (33510) covalent geometry : angle 0.57306 / 0.32 (45269) hydrogen bonds : bond 0.09121 / 6.12 ( 2517) hydrogen bonds : angle 3.94716 / 2.82 ( 7539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 405 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: B 78 MET cc_start: 0.8927 (mtt) cc_final: 0.8436 (mtt) REVERT: B 167 LYS cc_start: 0.8382 (tttm) cc_final: 0.8130 (tttt) REVERT: C 105 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7682 (mmp80) REVERT: E 42 ASP cc_start: 0.8671 (t0) cc_final: 0.8302 (t0) REVERT: G 125 ASP cc_start: 0.7870 (t0) cc_final: 0.7409 (t70) REVERT: H 103 TYR cc_start: 0.8879 (t80) cc_final: 0.8618 (t80) REVERT: J 59 GLU cc_start: 0.8186 (tp30) cc_final: 0.7981 (mt-10) REVERT: K 16 ILE cc_start: 0.8510 (mm) cc_final: 0.8040 (mm) REVERT: M 167 LYS cc_start: 0.9056 (tttm) cc_final: 0.8814 (tttm) REVERT: N 103 TYR cc_start: 0.8621 (t80) cc_final: 0.8391 (t80) REVERT: O 105 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7464 (mmp-170) REVERT: O 148 ASP cc_start: 0.8514 (m-30) cc_final: 0.8147 (m-30) REVERT: Q 79 LYS cc_start: 0.7585 (pttm) cc_final: 0.7155 (mtpt) REVERT: Q 100 GLN cc_start: 0.7970 (mt0) cc_final: 0.7752 (mt0) REVERT: Q 158 ASP cc_start: 0.7591 (m-30) cc_final: 0.7190 (m-30) REVERT: R 42 ASP cc_start: 0.8611 (t0) cc_final: 0.8334 (t0) REVERT: R 101 GLU cc_start: 0.7643 (tt0) cc_final: 0.7364 (tt0) REVERT: T 22 GLN cc_start: 0.7968 (tp40) cc_final: 0.7640 (tm-30) REVERT: W 167 LYS cc_start: 0.8101 (tttm) cc_final: 0.7848 (ttpt) REVERT: L 78 MET cc_start: 0.8551 (mtt) cc_final: 0.8163 (mtt) outliers start: 53 outliers final: 43 residues processed: 435 average time/residue: 0.1895 time to fit residues: 133.7249 Evaluate side-chains 435 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 392 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 100 GLN Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 300 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 371 optimal weight: 0.9980 chunk 320 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN E 22 GLN H 100 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102126 restraints weight = 314590.723| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 5.74 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 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 = 0.3326 r_free = 0.3326 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 (7 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 33510 Z= 0.127 Angle : 0.448 6.892 45269 Z= 0.256 Chirality : 0.037 0.174 4908 Planarity : 0.003 0.044 5822 Dihedral : 3.667 14.388 4330 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.05 % Allowed : 12.51 % Favored : 85.44 % 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: 2.36 (0.13), residues: 3992 helix: 2.31 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.35 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.019 0.001 TYR N 103 PHE 0.011 0.001 PHE S 131 TRP 0.006 0.001 TRP L 180 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (33510) covalent geometry : angle 0.44801 / 0.26 (45269) hydrogen bonds : bond 0.05865 / 3.92 ( 2517) hydrogen bonds : angle 3.30509 / 2.37 ( 7539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 431 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8750 (t0) cc_final: 0.8483 (m-40) REVERT: B 78 MET cc_start: 0.8874 (mtt) cc_final: 0.8508 (mtt) REVERT: B 167 LYS cc_start: 0.8332 (tttm) cc_final: 0.8089 (tttt) REVERT: C 22 GLN cc_start: 0.8154 (tt0) cc_final: 0.7825 (mt0) REVERT: C 105 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7460 (mmp80) REVERT: E 42 ASP cc_start: 0.8496 (t0) cc_final: 0.8079 (t0) REVERT: G 125 ASP cc_start: 0.7554 (t0) cc_final: 0.7129 (t70) REVERT: G 147 ASP cc_start: 0.8786 (t70) cc_final: 0.8467 (t70) REVERT: I 22 GLN cc_start: 0.7752 (tt0) cc_final: 0.7392 (mt0) REVERT: I 137 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8298 (ttp80) REVERT: J 59 GLU cc_start: 0.8180 (tp30) cc_final: 0.7878 (mt-10) REVERT: J 85 SER cc_start: 0.8948 (t) cc_final: 0.8113 (m) REVERT: J 169 MET cc_start: 0.7864 (ttm) cc_final: 0.7655 (ttm) REVERT: K 16 ILE cc_start: 0.8162 (mm) cc_final: 0.7571 (mm) REVERT: K 151 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7521 (mtmt) REVERT: M 135 TYR cc_start: 0.8614 (m-80) cc_final: 0.8391 (m-80) REVERT: M 167 LYS cc_start: 0.8981 (tttm) cc_final: 0.8598 (ttpp) REVERT: N 106 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8093 (mm-30) REVERT: O 105 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7329 (mmp80) REVERT: O 148 ASP cc_start: 0.8493 (m-30) cc_final: 0.8119 (m-30) REVERT: Q 79 LYS cc_start: 0.7488 (pttm) cc_final: 0.7051 (mtpt) REVERT: Q 130 TYR cc_start: 0.8940 (t80) cc_final: 0.8733 (t80) REVERT: Q 158 ASP cc_start: 0.7620 (m-30) cc_final: 0.7193 (m-30) REVERT: R 42 ASP cc_start: 0.8427 (t0) cc_final: 0.8160 (t0) REVERT: W 167 LYS cc_start: 0.7903 (tttm) cc_final: 0.7644 (ttpt) REVERT: L 78 MET cc_start: 0.8278 (mtt) cc_final: 0.7937 (mtt) outliers start: 41 outliers final: 35 residues processed: 454 average time/residue: 0.2000 time to fit residues: 147.7276 Evaluate side-chains 442 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 407 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 365 optimal weight: 0.0070 chunk 94 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN D 76 ASN E 22 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 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 = 0.3500 r_free = 0.3500 target = 0.112463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095494 restraints weight = 324630.004| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.66 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33510 Z= 0.187 Angle : 0.503 8.397 45269 Z= 0.285 Chirality : 0.040 0.180 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.729 14.489 4330 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.16 % Allowed : 13.05 % Favored : 84.79 % 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: 2.13 (0.13), residues: 3992 helix: 2.13 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.44 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.019 0.002 TYR M 24 PHE 0.013 0.001 PHE G 129 TRP 0.007 0.001 TRP Q 134 HIS 0.007 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (33510) covalent geometry : angle 0.50304 / 0.28 (45269) hydrogen bonds : bond 0.07623 / 5.11 ( 2517) hydrogen bonds : angle 3.60842 / 2.58 ( 7539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 418 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8804 (t0) cc_final: 0.8548 (m-40) REVERT: B 78 MET cc_start: 0.8846 (mtt) cc_final: 0.8354 (mtt) REVERT: B 167 LYS cc_start: 0.8422 (tttm) cc_final: 0.8176 (tttt) REVERT: C 105 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7574 (mmp80) REVERT: C 145 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: E 42 ASP cc_start: 0.8580 (t0) cc_final: 0.8207 (t0) REVERT: G 125 ASP cc_start: 0.7759 (t0) cc_final: 0.7320 (t70) REVERT: I 22 GLN cc_start: 0.7837 (tt0) cc_final: 0.7502 (mt0) REVERT: J 59 GLU cc_start: 0.8184 (tp30) cc_final: 0.7930 (mt-10) REVERT: K 16 ILE cc_start: 0.8340 (mm) cc_final: 0.7762 (mm) REVERT: K 151 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7575 (mtmt) REVERT: M 167 LYS cc_start: 0.9035 (tttm) cc_final: 0.8816 (tttm) REVERT: O 148 ASP cc_start: 0.8525 (m-30) cc_final: 0.8147 (m-30) REVERT: P 161 ILE cc_start: 0.7997 (mm) cc_final: 0.7795 (mt) REVERT: Q 158 ASP cc_start: 0.7560 (m-30) cc_final: 0.7164 (m-30) REVERT: R 42 ASP cc_start: 0.8493 (t0) cc_final: 0.8242 (t0) REVERT: R 101 GLU cc_start: 0.7545 (tt0) cc_final: 0.7274 (tt0) REVERT: W 167 LYS cc_start: 0.8055 (tttm) cc_final: 0.7803 (ttpt) REVERT: L 78 MET cc_start: 0.8473 (mtt) cc_final: 0.8108 (mtt) outliers start: 45 outliers final: 43 residues processed: 441 average time/residue: 0.1902 time to fit residues: 136.8899 Evaluate side-chains 447 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 403 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 236 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 335 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 327 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN D 76 ASN E 22 GLN H 17 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099155 restraints weight = 341166.302| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 5.85 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 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 = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33510 Z= 0.148 Angle : 0.468 8.543 45269 Z= 0.267 Chirality : 0.038 0.174 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.686 14.805 4330 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.08 % Allowed : 13.22 % Favored : 84.71 % 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: 2.34 (0.13), residues: 3992 helix: 2.28 (0.09), residues: 3142 sheet: None (None), residues: 0 loop : -1.34 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.019 0.001 TYR N 103 PHE 0.010 0.001 PHE S 131 TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (33510) covalent geometry : angle 0.46775 / 0.27 (45269) hydrogen bonds : bond 0.06747 / 4.52 ( 2517) hydrogen bonds : angle 3.44623 / 2.46 ( 7539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 410 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8780 (t0) cc_final: 0.8526 (m-40) REVERT: B 78 MET cc_start: 0.8865 (mtt) cc_final: 0.8418 (mtt) REVERT: B 167 LYS cc_start: 0.8397 (tttm) cc_final: 0.8146 (tttt) REVERT: C 22 GLN cc_start: 0.8198 (tt0) cc_final: 0.7856 (mt0) REVERT: C 105 ARG cc_start: 0.8122 (mmt90) cc_final: 0.7585 (mmp80) REVERT: C 145 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: E 42 ASP cc_start: 0.8566 (t0) cc_final: 0.8193 (t0) REVERT: G 125 ASP cc_start: 0.7652 (t0) cc_final: 0.7192 (t70) REVERT: G 147 ASP cc_start: 0.8743 (t70) cc_final: 0.8405 (t70) REVERT: I 22 GLN cc_start: 0.7800 (tt0) cc_final: 0.7481 (mt0) REVERT: J 59 GLU cc_start: 0.8185 (tp30) cc_final: 0.7891 (mt-10) REVERT: J 85 SER cc_start: 0.8955 (t) cc_final: 0.8112 (m) REVERT: K 16 ILE cc_start: 0.8257 (mm) cc_final: 0.7681 (mm) REVERT: K 151 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7597 (mtmt) REVERT: M 167 LYS cc_start: 0.9015 (tttm) cc_final: 0.8650 (ttpp) REVERT: O 148 ASP cc_start: 0.8535 (m-30) cc_final: 0.8158 (m-30) REVERT: P 161 ILE cc_start: 0.7974 (mm) cc_final: 0.7766 (mt) REVERT: Q 158 ASP cc_start: 0.7586 (m-30) cc_final: 0.7181 (m-30) REVERT: R 42 ASP cc_start: 0.8458 (t0) cc_final: 0.8193 (t0) REVERT: W 167 LYS cc_start: 0.8037 (tttm) cc_final: 0.7767 (ttpt) REVERT: L 78 MET cc_start: 0.8415 (mtt) cc_final: 0.8071 (mtt) outliers start: 42 outliers final: 38 residues processed: 431 average time/residue: 0.1874 time to fit residues: 131.0579 Evaluate side-chains 441 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN B 22 GLN E 22 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099466 restraints weight = 328376.196| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.80 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33510 Z= 0.149 Angle : 0.472 8.465 45269 Z= 0.268 Chirality : 0.039 0.194 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.677 15.533 4330 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.99 % Allowed : 13.27 % Favored : 84.74 % 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: 2.37 (0.13), residues: 3992 helix: 2.30 (0.09), residues: 3142 sheet: None (None), residues: 0 loop : -1.32 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.018 0.001 TYR N 103 PHE 0.010 0.001 PHE T 129 TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (33510) covalent geometry : angle 0.47153 / 0.27 (45269) hydrogen bonds : bond 0.06736 / 4.51 ( 2517) hydrogen bonds : angle 3.44235 / 2.46 ( 7539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8764 (t0) cc_final: 0.8504 (m-40) REVERT: B 78 MET cc_start: 0.8932 (mtt) cc_final: 0.8387 (mtt) REVERT: B 167 LYS cc_start: 0.8373 (tttm) cc_final: 0.8116 (tttt) REVERT: C 22 GLN cc_start: 0.8221 (tt0) cc_final: 0.7864 (mt0) REVERT: C 105 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7500 (mmp80) REVERT: C 145 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: G 125 ASP cc_start: 0.7624 (t0) cc_final: 0.7179 (t70) REVERT: G 147 ASP cc_start: 0.8754 (t70) cc_final: 0.8423 (t70) REVERT: I 22 GLN cc_start: 0.7809 (tt0) cc_final: 0.7497 (mt0) REVERT: J 59 GLU cc_start: 0.8193 (tp30) cc_final: 0.7865 (mt-10) REVERT: J 85 SER cc_start: 0.8955 (t) cc_final: 0.8106 (m) REVERT: K 16 ILE cc_start: 0.8244 (mm) cc_final: 0.7667 (mm) REVERT: K 151 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7451 (mtmt) REVERT: M 167 LYS cc_start: 0.9013 (tttm) cc_final: 0.8636 (ttpp) REVERT: O 148 ASP cc_start: 0.8509 (m-30) cc_final: 0.8123 (m-30) REVERT: P 161 ILE cc_start: 0.7953 (mm) cc_final: 0.7749 (mt) REVERT: Q 158 ASP cc_start: 0.7582 (m-30) cc_final: 0.7162 (m-30) REVERT: R 42 ASP cc_start: 0.8450 (t0) cc_final: 0.8184 (t0) REVERT: R 101 GLU cc_start: 0.7443 (tt0) cc_final: 0.7147 (tt0) REVERT: W 167 LYS cc_start: 0.7964 (tttm) cc_final: 0.7675 (ttpt) REVERT: L 78 MET cc_start: 0.8401 (mtt) cc_final: 0.8057 (mtt) outliers start: 39 outliers final: 37 residues processed: 432 average time/residue: 0.1950 time to fit residues: 137.2997 Evaluate side-chains 444 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 406 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 366 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN E 22 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098952 restraints weight = 311365.406| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 5.64 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33510 Z= 0.143 Angle : 0.467 8.435 45269 Z= 0.265 Chirality : 0.038 0.187 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.661 15.981 4330 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.05 % Allowed : 13.33 % Favored : 84.62 % 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: 2.44 (0.13), residues: 3992 helix: 2.34 (0.09), residues: 3142 sheet: None (None), residues: 0 loop : -1.29 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.019 0.001 TYR N 103 PHE 0.010 0.001 PHE T 129 TRP 0.007 0.001 TRP P 180 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (33510) covalent geometry : angle 0.46728 / 0.27 (45269) hydrogen bonds : bond 0.06544 / 4.38 ( 2517) hydrogen bonds : angle 3.39268 / 2.43 ( 7539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5542.49 seconds wall clock time: 96 minutes 24.91 seconds (5784.91 seconds total)