Starting phenix.real_space_refine on Tue Aug 26 01:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_37759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_37759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_37759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_37759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr0_37759/08_2025/8wr0_37759.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 12.08, per 1000 atoms: 0.37 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: 2.83 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.84 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: 5.48 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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 2.260 nonbonded pdb=" OD2 ASP W 138 " pdb="FE FE W 201 " model vdw 1.922 2.260 nonbonded pdb=" OD2 ASP I 138 " pdb="FE FE I 201 " model vdw 1.936 2.260 nonbonded pdb=" OD2 ASP H 138 " pdb="FE FE H 201 " model vdw 1.941 2.260 nonbonded pdb=" OD2 ASP F 138 " pdb="FE FE F 201 " model vdw 1.942 2.260 ... (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: 0.930 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 32.110 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 aren 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 covalent geometry : bond 0.00579 (33510) covalent geometry : angle 0.57787 (45269) hydrogen bonds : bond 0.13919 ( 2517) hydrogen bonds : angle 5.00836 ( 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 : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASP cc_start: 0.8070 (t70) cc_final: 0.7657 (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: 0.8055 (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: 0.7780 (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: 0.7796 (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: 0.2108 time to fit residues: 196.1636 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 : 1.280 ------------------------------------------------------------------------------- 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: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 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: 0.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 76 ASN X 17 ASN X 22 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100492 restraints weight = 349783.822| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 5.80 r_work (final): 0.3317 ------------------------------------------------------------------------------- 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33510 Z= 0.141 Angle : 0.477 7.562 45269 Z= 0.271 Chirality : 0.039 0.164 4908 Planarity : 0.003 0.041 5822 Dihedral : 3.852 14.731 4332 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.46 % Allowed : 7.35 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.13), residues: 3992 helix: 1.25 (0.09), residues: 3128 sheet: None (None), residues: 0 loop : -2.16 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 105 TYR 0.016 0.001 TYR K 24 PHE 0.013 0.001 PHE S 131 TRP 0.007 0.001 TRP K 180 HIS 0.008 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00261 (33510) covalent geometry : angle 0.47665 (45269) hydrogen bonds : bond 0.06588 ( 2517) hydrogen bonds : angle 3.59752 ( 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 563 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 541 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8729 (m-10) cc_final: 0.8487 (m-80) REVERT: B 76 ASN cc_start: 0.8205 (p0) cc_final: 0.7714 (p0) REVERT: B 78 MET cc_start: 0.8965 (mtt) cc_final: 0.8624 (mtt) REVERT: B 167 LYS cc_start: 0.8377 (tttm) cc_final: 0.8149 (tttt) REVERT: B 169 MET cc_start: 0.8501 (ttm) cc_final: 0.8265 (mtp) REVERT: C 105 ARG cc_start: 0.7989 (mmt90) cc_final: 0.7480 (mmp80) REVERT: D 148 ASP cc_start: 0.8347 (t0) cc_final: 0.8099 (t0) REVERT: D 169 MET cc_start: 0.8791 (ttm) cc_final: 0.8433 (ttm) REVERT: G 147 ASP cc_start: 0.8714 (t70) cc_final: 0.8443 (t70) REVERT: I 22 GLN cc_start: 0.7865 (tt0) cc_final: 0.7530 (mt0) REVERT: J 75 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7940 (mtt90) REVERT: K 16 ILE cc_start: 0.8307 (mm) cc_final: 0.7724 (mm) REVERT: K 105 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7986 (mmt90) REVERT: K 151 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7653 (mtmt) REVERT: M 167 LYS cc_start: 0.9002 (tttm) cc_final: 0.8795 (tttm) REVERT: O 67 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7304 (tm-30) REVERT: O 105 ARG cc_start: 0.7653 (mmt90) cc_final: 0.7401 (mmp-170) REVERT: O 148 ASP cc_start: 0.8598 (m-30) cc_final: 0.8317 (m-30) REVERT: Q 25 LYS cc_start: 0.8094 (tttp) cc_final: 0.7732 (tttt) REVERT: R 42 ASP cc_start: 0.8520 (t0) cc_final: 0.8243 (t0) REVERT: S 55 GLN cc_start: 0.7970 (tp40) cc_final: 0.7656 (tp-100) REVERT: V 56 HIS cc_start: 0.7751 (t70) cc_final: 0.7456 (t70) REVERT: W 147 ASP cc_start: 0.8658 (t70) cc_final: 0.8317 (t0) REVERT: W 167 LYS cc_start: 0.8006 (tttm) cc_final: 0.7744 (ttpt) REVERT: W 169 MET cc_start: 0.8180 (ttm) cc_final: 0.7842 (ttm) REVERT: X 91 ILE cc_start: 0.9192 (mp) cc_final: 0.8983 (mp) REVERT: L 78 MET cc_start: 0.8464 (mtt) cc_final: 0.8090 (mtt) outliers start: 22 outliers final: 13 residues processed: 551 average time/residue: 0.2059 time to fit residues: 182.5513 Evaluate side-chains 454 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 441 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 2.9990 chunk 101 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN C 76 ASN E 17 ASN E 22 GLN F 76 ASN H 157 ASN J 17 ASN J 23 HIS K 76 ASN ** 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 22 GLN X 76 ASN L 39 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095452 restraints weight = 333931.627| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.69 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33510 Z= 0.196 Angle : 0.518 6.646 45269 Z= 0.293 Chirality : 0.040 0.185 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.832 14.403 4330 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.96 % Allowed : 9.85 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.13), residues: 3992 helix: 1.51 (0.09), residues: 3133 sheet: None (None), residues: 0 loop : -2.00 (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 0.013 0.001 PHE N 131 TRP 0.006 0.001 TRP Q 134 HIS 0.006 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00438 (33510) covalent geometry : angle 0.51794 (45269) hydrogen bonds : bond 0.07940 ( 2517) hydrogen bonds : angle 3.76843 ( 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 480 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 439 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8803 (m-10) cc_final: 0.8524 (m-80) REVERT: B 76 ASN cc_start: 0.8307 (p0) cc_final: 0.8046 (p0) REVERT: B 78 MET cc_start: 0.9014 (mtt) cc_final: 0.8660 (mtt) REVERT: B 100 GLN cc_start: 0.8390 (mt0) cc_final: 0.7797 (mt0) REVERT: B 167 LYS cc_start: 0.8362 (tttm) cc_final: 0.8112 (tttt) REVERT: C 78 MET cc_start: 0.8486 (mtt) cc_final: 0.7908 (mtt) REVERT: C 105 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7503 (mmp80) REVERT: D 145 GLU cc_start: 0.8113 (tt0) cc_final: 0.7867 (tt0) REVERT: G 147 ASP cc_start: 0.8774 (t70) cc_final: 0.8463 (t70) REVERT: I 22 GLN cc_start: 0.7873 (tt0) cc_final: 0.7539 (mt0) REVERT: K 16 ILE cc_start: 0.8464 (mm) cc_final: 0.7808 (mm) REVERT: K 105 ARG cc_start: 0.8255 (mmt90) cc_final: 0.8036 (mmt90) REVERT: K 151 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7715 (mtmt) REVERT: M 167 LYS cc_start: 0.9019 (tttm) cc_final: 0.8790 (tttm) REVERT: O 105 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7445 (mmp-170) REVERT: O 148 ASP cc_start: 0.8536 (m-30) cc_final: 0.8246 (m-30) REVERT: R 42 ASP cc_start: 0.8551 (t0) cc_final: 0.8275 (t0) REVERT: T 22 GLN cc_start: 0.7888 (tp40) cc_final: 0.7546 (tm-30) REVERT: V 56 HIS cc_start: 0.7838 (t70) cc_final: 0.7578 (t70) REVERT: W 167 LYS cc_start: 0.7997 (tttm) cc_final: 0.7715 (ttpt) REVERT: L 78 MET cc_start: 0.8444 (mtt) cc_final: 0.8014 (mtt) outliers start: 41 outliers final: 30 residues processed: 460 average time/residue: 0.2041 time to fit residues: 152.4894 Evaluate side-chains 447 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 417 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 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 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 N residue 58 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 70 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 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: 0.9990 chunk 169 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN C 76 ASN E 22 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 17 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 = 0.3563 r_free = 0.3563 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100642 restraints weight = 322999.344| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 5.63 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33510 Z= 0.131 Angle : 0.448 6.153 45269 Z= 0.255 Chirality : 0.038 0.184 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.680 14.117 4330 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.68 % Allowed : 11.17 % Favored : 87.15 % 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 aren not related in a simple way. whole: 1.89 (0.13), residues: 3992 helix: 2.02 (0.09), residues: 3129 sheet: None (None), residues: 0 loop : -1.69 (0.16), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 137 TYR 0.016 0.001 TYR K 24 PHE 0.011 0.001 PHE S 131 TRP 0.005 0.001 TRP Q 134 HIS 0.006 0.001 HIS S 39 Details of bonding type rmsd covalent geometry : bond 0.00258 (33510) covalent geometry : angle 0.44789 (45269) hydrogen bonds : bond 0.06130 ( 2517) hydrogen bonds : angle 3.37239 ( 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 492 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 462 time to evaluate : 1.320 Fit side-chains REVERT: A 37 TYR cc_start: 0.8716 (m-10) cc_final: 0.8460 (m-80) REVERT: B 78 MET cc_start: 0.8886 (mtt) cc_final: 0.8571 (mtt) REVERT: B 167 LYS cc_start: 0.8383 (tttm) cc_final: 0.8140 (tttt) REVERT: C 22 GLN cc_start: 0.8134 (tt0) cc_final: 0.7821 (mt0) REVERT: C 105 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7459 (mmp80) REVERT: D 145 GLU cc_start: 0.7987 (tt0) cc_final: 0.7617 (mt-10) REVERT: F 78 MET cc_start: 0.8751 (mtt) cc_final: 0.8498 (mtt) REVERT: G 147 ASP cc_start: 0.8761 (t70) cc_final: 0.8530 (t0) REVERT: I 22 GLN cc_start: 0.7795 (tt0) cc_final: 0.7504 (mt0) REVERT: J 75 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7871 (mtt90) REVERT: K 16 ILE cc_start: 0.8290 (mm) cc_final: 0.7690 (mm) REVERT: K 59 GLU cc_start: 0.8245 (tp30) cc_final: 0.7869 (mt-10) REVERT: K 151 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7605 (mtmt) REVERT: M 151 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7889 (ptpp) REVERT: M 167 LYS cc_start: 0.8994 (tttm) cc_final: 0.8779 (tttm) REVERT: O 105 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7334 (mmp-170) REVERT: O 148 ASP cc_start: 0.8464 (m-30) cc_final: 0.8131 (m-30) REVERT: R 42 ASP cc_start: 0.8432 (t0) cc_final: 0.8157 (t0) REVERT: V 56 HIS cc_start: 0.7856 (t70) cc_final: 0.7627 (t70) REVERT: V 106 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8404 (mm-30) REVERT: W 167 LYS cc_start: 0.7988 (tttm) cc_final: 0.7707 (ttpt) REVERT: W 169 MET cc_start: 0.7954 (ttm) cc_final: 0.7579 (ttm) REVERT: L 78 MET cc_start: 0.8315 (mtt) cc_final: 0.7946 (mtt) outliers start: 30 outliers final: 19 residues processed: 479 average time/residue: 0.1945 time to fit residues: 151.1162 Evaluate side-chains 449 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 430 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 170 VAL 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 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 62 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain W residue 58 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: 7.9990 chunk 242 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 22 GLN D 76 ASN D 154 ASN E 22 GLN H 76 ASN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099597 restraints weight = 368296.727| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 5.93 r_work (final): 0.3313 ------------------------------------------------------------------------------- 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 = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33510 Z= 0.138 Angle : 0.450 6.103 45269 Z= 0.256 Chirality : 0.038 0.163 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.626 14.243 4330 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.19 % Allowed : 11.67 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.13), residues: 3992 helix: 2.16 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.53 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 75 TYR 0.016 0.001 TYR K 24 PHE 0.010 0.001 PHE S 131 TRP 0.005 0.001 TRP Q 134 HIS 0.005 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00280 (33510) covalent geometry : angle 0.44984 (45269) hydrogen bonds : bond 0.06338 ( 2517) hydrogen bonds : angle 3.36166 ( 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 481 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 434 time to evaluate : 1.393 Fit side-chains REVERT: A 37 TYR cc_start: 0.8722 (m-10) cc_final: 0.8461 (m-80) REVERT: B 78 MET cc_start: 0.8918 (mtt) cc_final: 0.8607 (mtt) REVERT: B 167 LYS cc_start: 0.8402 (tttm) cc_final: 0.8159 (tttt) REVERT: C 22 GLN cc_start: 0.8148 (tt0) cc_final: 0.7834 (mt0) REVERT: C 105 ARG cc_start: 0.8012 (mmt90) cc_final: 0.7465 (mmp80) REVERT: D 145 GLU cc_start: 0.7965 (tt0) cc_final: 0.7613 (mt-10) REVERT: F 78 MET cc_start: 0.8800 (mtt) cc_final: 0.8531 (mtt) REVERT: G 125 ASP cc_start: 0.7647 (t0) cc_final: 0.7258 (t70) REVERT: G 147 ASP cc_start: 0.8766 (t70) cc_final: 0.8527 (t70) REVERT: I 22 GLN cc_start: 0.7791 (tt0) cc_final: 0.7444 (mt0) REVERT: K 16 ILE cc_start: 0.8307 (mm) cc_final: 0.7709 (mm) REVERT: K 59 GLU cc_start: 0.8170 (tp30) cc_final: 0.7931 (mt-10) REVERT: K 151 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7565 (mtmt) REVERT: M 151 LYS cc_start: 0.8558 (ptpt) cc_final: 0.7916 (ptpp) REVERT: M 167 LYS cc_start: 0.8982 (tttm) cc_final: 0.8733 (ttmt) REVERT: N 47 MET cc_start: 0.8829 (mmm) cc_final: 0.8557 (mmt) REVERT: O 105 ARG cc_start: 0.7649 (mmt90) cc_final: 0.7332 (mmp-170) REVERT: O 148 ASP cc_start: 0.8521 (m-30) cc_final: 0.8180 (m-30) REVERT: R 42 ASP cc_start: 0.8448 (t0) cc_final: 0.8188 (t0) REVERT: S 47 MET cc_start: 0.8655 (mmm) cc_final: 0.7827 (mmt) REVERT: V 56 HIS cc_start: 0.7873 (t70) cc_final: 0.7657 (t70) REVERT: W 167 LYS cc_start: 0.8028 (tttm) cc_final: 0.7727 (ttpt) REVERT: W 169 MET cc_start: 0.7966 (ttm) cc_final: 0.7684 (ttm) REVERT: L 78 MET cc_start: 0.8287 (mtt) cc_final: 0.7898 (mtt) outliers start: 47 outliers final: 38 residues processed: 460 average time/residue: 0.2231 time to fit residues: 166.0296 Evaluate side-chains 450 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 412 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 17 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 H residue 76 ASN 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 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 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 62 LEU Chi-restraints excluded: chain R residue 70 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 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 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: 0.9990 chunk 48 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 143 optimal weight: 0.4980 chunk 344 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN D 76 ASN E 22 GLN H 76 ASN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS U 55 GLN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098565 restraints weight = 324473.506| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 5.66 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33510 Z= 0.152 Angle : 0.460 6.282 45269 Z= 0.262 Chirality : 0.039 0.186 4908 Planarity : 0.003 0.047 5822 Dihedral : 3.638 14.405 4330 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.16 % Allowed : 11.98 % Favored : 85.86 % 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 aren not related in a simple way. whole: 2.20 (0.13), residues: 3992 helix: 2.20 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.43 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.016 0.001 TYR K 24 PHE 0.011 0.001 PHE G 129 TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00323 (33510) covalent geometry : angle 0.45955 (45269) hydrogen bonds : bond 0.06707 ( 2517) hydrogen bonds : angle 3.41386 ( 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 471 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 426 time to evaluate : 1.326 Fit side-chains REVERT: A 37 TYR cc_start: 0.8760 (m-10) cc_final: 0.8503 (m-80) REVERT: A 107 ASN cc_start: 0.8743 (t0) cc_final: 0.8459 (m-40) REVERT: B 78 MET cc_start: 0.8903 (mtt) cc_final: 0.8478 (mtt) REVERT: B 167 LYS cc_start: 0.8394 (tttm) cc_final: 0.8145 (tttt) REVERT: C 22 GLN cc_start: 0.8191 (tt0) cc_final: 0.7853 (mt0) REVERT: C 105 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7483 (mmp80) REVERT: D 145 GLU cc_start: 0.7979 (tt0) cc_final: 0.7606 (mt-10) REVERT: G 125 ASP cc_start: 0.7769 (t0) cc_final: 0.7376 (t70) REVERT: G 147 ASP cc_start: 0.8772 (t70) cc_final: 0.8473 (t0) REVERT: I 22 GLN cc_start: 0.7806 (tt0) cc_final: 0.7443 (mt0) REVERT: K 16 ILE cc_start: 0.8266 (mm) cc_final: 0.7654 (mm) REVERT: K 151 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7561 (mtmt) REVERT: M 151 LYS cc_start: 0.8546 (ptpt) cc_final: 0.7910 (ptpp) REVERT: M 167 LYS cc_start: 0.8992 (tttm) cc_final: 0.8744 (ttmt) REVERT: N 47 MET cc_start: 0.8839 (mmm) cc_final: 0.8550 (mmt) REVERT: O 105 ARG cc_start: 0.7671 (mmt90) cc_final: 0.7466 (mmp80) REVERT: O 148 ASP cc_start: 0.8562 (m-30) cc_final: 0.8197 (m-30) REVERT: R 42 ASP cc_start: 0.8423 (t0) cc_final: 0.8167 (t0) REVERT: W 167 LYS cc_start: 0.8024 (tttm) cc_final: 0.7725 (ttpt) REVERT: W 169 MET cc_start: 0.7979 (ttm) cc_final: 0.7697 (ttm) REVERT: L 78 MET cc_start: 0.8280 (mtt) cc_final: 0.7827 (mtt) outliers start: 45 outliers final: 42 residues processed: 452 average time/residue: 0.1994 time to fit residues: 146.6749 Evaluate side-chains 453 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 411 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain E residue 17 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 H residue 76 ASN 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 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 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 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 62 LEU 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 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 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 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: 0.9980 chunk 102 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 366 optimal weight: 0.0050 chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN D 76 ASN E 22 GLN H 17 ASN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN M 17 ASN M 154 ASN O 27 ASN R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104955 restraints weight = 311922.637| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.60 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33510 Z= 0.111 Angle : 0.420 7.124 45269 Z= 0.240 Chirality : 0.037 0.171 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.532 13.854 4330 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.71 % Allowed : 12.68 % Favored : 85.61 % 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 aren not related in a simple way. whole: 2.65 (0.13), residues: 3992 helix: 2.51 (0.09), residues: 3130 sheet: None (None), residues: 0 loop : -1.24 (0.17), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 75 TYR 0.016 0.001 TYR K 24 PHE 0.010 0.001 PHE S 131 TRP 0.005 0.001 TRP P 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00202 (33510) covalent geometry : angle 0.41983 (45269) hydrogen bonds : bond 0.05067 ( 2517) hydrogen bonds : angle 3.10270 ( 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 509 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 480 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8658 (m-10) cc_final: 0.8395 (m-80) REVERT: A 107 ASN cc_start: 0.8752 (t0) cc_final: 0.8496 (m-40) REVERT: B 167 LYS cc_start: 0.8386 (tttm) cc_final: 0.8144 (tttt) REVERT: C 105 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7435 (mmp80) REVERT: G 125 ASP cc_start: 0.7521 (t0) cc_final: 0.7129 (t70) REVERT: G 147 ASP cc_start: 0.8669 (t70) cc_final: 0.8434 (t0) REVERT: I 78 MET cc_start: 0.8252 (mtt) cc_final: 0.7498 (mtt) REVERT: J 85 SER cc_start: 0.8941 (t) cc_final: 0.8271 (m) REVERT: K 16 ILE cc_start: 0.8013 (mm) cc_final: 0.7493 (mm) REVERT: K 59 GLU cc_start: 0.8121 (tp30) cc_final: 0.7816 (mt-10) REVERT: K 151 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7583 (mtmt) REVERT: M 144 THR cc_start: 0.8865 (t) cc_final: 0.8616 (m) REVERT: M 167 LYS cc_start: 0.8936 (tttm) cc_final: 0.8569 (ttpp) REVERT: N 47 MET cc_start: 0.8647 (mmm) cc_final: 0.8417 (mmt) REVERT: N 106 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8063 (mm-30) REVERT: O 105 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7393 (mmp80) REVERT: O 148 ASP cc_start: 0.8444 (m-30) cc_final: 0.8084 (m-30) REVERT: P 161 ILE cc_start: 0.8005 (mm) cc_final: 0.7769 (mt) REVERT: R 59 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8054 (tp30) REVERT: W 163 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8089 (mm-30) REVERT: W 167 LYS cc_start: 0.7990 (tttm) cc_final: 0.7705 (ttpt) REVERT: L 78 MET cc_start: 0.8182 (mtt) cc_final: 0.7829 (mtt) outliers start: 29 outliers final: 23 residues processed: 498 average time/residue: 0.1932 time to fit residues: 158.0258 Evaluate side-chains 449 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 426 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain G 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 93 SER Chi-restraints excluded: chain K residue 93 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 62 LEU 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 V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain X residue 17 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 319 optimal weight: 3.9990 chunk 365 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN D 39 HIS E 17 ASN E 22 GLN H 14 ASN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS M 154 ASN Q 14 ASN R 56 HIS ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 22 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098317 restraints weight = 327184.647| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.70 r_work (final): 0.3290 ------------------------------------------------------------------------------- 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: 9 | |-----------------------------------------------------------------------------| |-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: 9 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33510 Z= 0.161 Angle : 0.480 7.425 45269 Z= 0.272 Chirality : 0.039 0.178 4908 Planarity : 0.003 0.047 5822 Dihedral : 3.612 16.358 4330 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.80 % Allowed : 13.55 % Favored : 84.65 % 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 aren not related in a simple way. whole: 2.44 (0.13), residues: 3992 helix: 2.34 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -1.28 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.018 0.001 TYR M 24 PHE 0.013 0.001 PHE G 129 TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00346 (33510) covalent geometry : angle 0.48042 (45269) hydrogen bonds : bond 0.06818 ( 2517) hydrogen bonds : angle 3.40327 ( 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 453 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 421 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8776 (m-10) cc_final: 0.8505 (m-80) REVERT: A 107 ASN cc_start: 0.8781 (t0) cc_final: 0.8534 (m-40) REVERT: B 167 LYS cc_start: 0.8399 (tttm) cc_final: 0.8136 (tttt) REVERT: C 22 GLN cc_start: 0.8205 (tt0) cc_final: 0.7869 (mt0) REVERT: C 105 ARG cc_start: 0.8084 (mmt90) cc_final: 0.7522 (mmp80) REVERT: G 125 ASP cc_start: 0.7701 (t0) cc_final: 0.7308 (t70) REVERT: G 147 ASP cc_start: 0.8751 (t70) cc_final: 0.8503 (t0) REVERT: I 22 GLN cc_start: 0.7801 (tt0) cc_final: 0.7495 (mt0) REVERT: J 85 SER cc_start: 0.9094 (t) cc_final: 0.8206 (m) REVERT: K 16 ILE cc_start: 0.8218 (mm) cc_final: 0.7609 (mm) REVERT: K 59 GLU cc_start: 0.8147 (tp30) cc_final: 0.7889 (mt-10) REVERT: K 151 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7432 (mttt) REVERT: M 167 LYS cc_start: 0.9009 (tttm) cc_final: 0.8771 (ttmt) REVERT: N 47 MET cc_start: 0.8866 (mmm) cc_final: 0.8557 (mmt) REVERT: N 106 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8147 (mm-30) REVERT: O 148 ASP cc_start: 0.8554 (m-30) cc_final: 0.8177 (m-30) REVERT: R 59 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8108 (tp30) REVERT: W 163 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8140 (mm-30) REVERT: W 167 LYS cc_start: 0.8002 (tttm) cc_final: 0.7744 (ttpt) REVERT: L 78 MET cc_start: 0.8309 (mtt) cc_final: 0.7876 (mtt) outliers start: 32 outliers final: 27 residues processed: 439 average time/residue: 0.2127 time to fit residues: 151.4385 Evaluate side-chains 440 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 413 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain G 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 93 SER Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 93 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 62 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 236 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN B 22 GLN D 76 ASN E 22 GLN H 14 ASN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 22 GLN X 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093539 restraints weight = 344077.323| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 5.76 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 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 = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33510 Z= 0.238 Angle : 0.560 7.221 45269 Z= 0.315 Chirality : 0.042 0.186 4908 Planarity : 0.003 0.048 5822 Dihedral : 3.857 16.150 4330 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.96 % Allowed : 13.44 % Favored : 84.60 % 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 aren not related in a simple way. whole: 1.94 (0.13), residues: 3992 helix: 1.97 (0.09), residues: 3138 sheet: None (None), residues: 0 loop : -1.37 (0.17), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.020 0.002 TYR M 24 PHE 0.014 0.002 PHE N 131 TRP 0.009 0.001 TRP P 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00549 (33510) covalent geometry : angle 0.55990 (45269) hydrogen bonds : bond 0.08777 ( 2517) hydrogen bonds : angle 3.85405 ( 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: 38 poor density : 414 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8867 (m-10) cc_final: 0.8593 (m-80) REVERT: A 107 ASN cc_start: 0.8802 (t0) cc_final: 0.8473 (m-40) REVERT: B 100 GLN cc_start: 0.8456 (mt0) cc_final: 0.7920 (mt0) REVERT: B 167 LYS cc_start: 0.8389 (tttm) cc_final: 0.8144 (tttt) REVERT: C 105 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7706 (mmp80) REVERT: E 47 MET cc_start: 0.8787 (mtt) cc_final: 0.8275 (mtt) REVERT: G 125 ASP cc_start: 0.7854 (t0) cc_final: 0.7422 (t70) REVERT: H 103 TYR cc_start: 0.8859 (t80) cc_final: 0.8594 (t80) REVERT: K 16 ILE cc_start: 0.8432 (mm) cc_final: 0.7972 (mm) REVERT: M 167 LYS cc_start: 0.9047 (tttm) cc_final: 0.8803 (ttmt) REVERT: O 148 ASP cc_start: 0.8546 (m-30) cc_final: 0.8168 (m-30) REVERT: Q 158 ASP cc_start: 0.7631 (m-30) cc_final: 0.7219 (m-30) REVERT: R 101 GLU cc_start: 0.7637 (tt0) cc_final: 0.7345 (tt0) REVERT: W 167 LYS cc_start: 0.8062 (tttm) cc_final: 0.7786 (ttpt) REVERT: L 78 MET cc_start: 0.8440 (mtt) cc_final: 0.7995 (mtt) outliers start: 38 outliers final: 35 residues processed: 437 average time/residue: 0.2254 time to fit residues: 159.2955 Evaluate side-chains 432 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 397 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 151 LYS 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 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 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 58 SER 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 Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 62 LEU 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 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 Chi-restraints excluded: chain X residue 76 ASN 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: 10.0000 chunk 13 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN E 22 GLN G 22 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096667 restraints weight = 329187.809| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 5.70 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33510 Z= 0.165 Angle : 0.498 7.289 45269 Z= 0.282 Chirality : 0.039 0.187 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.788 16.397 4330 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.85 % Allowed : 13.69 % Favored : 84.46 % 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 aren not related in a simple way. whole: 2.19 (0.13), residues: 3992 helix: 2.16 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 137 TYR 0.023 0.001 TYR N 103 PHE 0.011 0.001 PHE T 129 TRP 0.007 0.001 TRP P 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00347 (33510) covalent geometry : angle 0.49753 (45269) hydrogen bonds : bond 0.07402 ( 2517) hydrogen bonds : angle 3.58357 ( 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 442 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 408 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8784 (m-10) cc_final: 0.8531 (m-80) REVERT: A 107 ASN cc_start: 0.8811 (t0) cc_final: 0.8509 (m-40) REVERT: B 167 LYS cc_start: 0.8384 (tttm) cc_final: 0.8135 (tttt) REVERT: C 105 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7655 (mmp80) REVERT: E 47 MET cc_start: 0.8600 (mtt) cc_final: 0.8055 (mtt) REVERT: G 125 ASP cc_start: 0.7716 (t0) cc_final: 0.7267 (t70) REVERT: I 22 GLN cc_start: 0.7887 (tt0) cc_final: 0.7515 (mt0) REVERT: K 16 ILE cc_start: 0.8324 (mm) cc_final: 0.7819 (mm) REVERT: K 151 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7603 (mtmt) REVERT: M 167 LYS cc_start: 0.9008 (tttm) cc_final: 0.8770 (ttmt) REVERT: N 47 MET cc_start: 0.8871 (mmm) cc_final: 0.8559 (mmt) REVERT: O 148 ASP cc_start: 0.8555 (m-30) cc_final: 0.8185 (m-30) REVERT: Q 158 ASP cc_start: 0.7574 (m-30) cc_final: 0.7181 (m-30) REVERT: R 101 GLU cc_start: 0.7530 (tt0) cc_final: 0.7243 (tt0) REVERT: W 163 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8225 (mm-30) REVERT: W 167 LYS cc_start: 0.7927 (tttm) cc_final: 0.7643 (ttpt) REVERT: L 78 MET cc_start: 0.8408 (mtt) cc_final: 0.7985 (mtt) outliers start: 34 outliers final: 32 residues processed: 429 average time/residue: 0.2247 time to fit residues: 155.6021 Evaluate side-chains 430 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 398 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 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 I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 58 SER 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 Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 62 LEU 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 V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER 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: 0.9990 chunk 227 optimal weight: 0.9980 chunk 341 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN D 76 ASN E 22 GLN H 157 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101846 restraints weight = 314370.143| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 5.62 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 33510 Z= 0.124 Angle : 0.451 7.747 45269 Z= 0.256 Chirality : 0.038 0.173 4908 Planarity : 0.003 0.044 5822 Dihedral : 3.630 15.800 4330 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.77 % Allowed : 13.83 % Favored : 84.40 % 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 aren not related in a simple way. whole: 2.65 (0.13), residues: 3992 helix: 2.48 (0.09), residues: 3142 sheet: None (None), residues: 0 loop : -1.19 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 137 TYR 0.021 0.001 TYR N 103 PHE 0.011 0.001 PHE T 129 TRP 0.007 0.001 TRP P 134 HIS 0.008 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00237 (33510) covalent geometry : angle 0.45104 (45269) hydrogen bonds : bond 0.05672 ( 2517) hydrogen bonds : angle 3.22393 ( 7539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5968.24 seconds wall clock time: 103 minutes 41.44 seconds (6221.44 seconds total)