Starting phenix.real_space_refine on Thu May 29 19:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr0_37759/05_2025/8wr0_37759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr0_37759/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wr0_37759/05_2025/8wr0_37759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr0_37759/05_2025/8wr0_37759.map" model { file = "/net/cci-nas-00/data/ceres_data/8wr0_37759/05_2025/8wr0_37759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr0_37759/05_2025/8wr0_37759.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 32.89, per 1000 atoms: 1.00 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: 8.54 Conformation dependent library (CDL) restraints added in 7.6 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 12 sheets defined 82.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 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: 10.48 Time building geometry restraints manager: 9.70 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 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 181 \ or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 87.660 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.170 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP G 134 HIS 0.006 0.001 HIS E 65 PHE 0.016 0.002 PHE N 131 TYR 0.020 0.002 TYR K 24 ARG 0.005 0.001 ARG G 110 Details of bonding type rmsd hydrogen bonds : bond 0.13919 ( 2517) hydrogen bonds : angle 5.00836 ( 7539) covalent geometry : bond 0.00579 (33510) covalent geometry : angle 0.57787 (45269) *********************** 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 : 3.692 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: 0.4734 time to fit residues: 435.0406 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 : 3.670 ------------------------------------------------------------------------------- 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 324 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 0.0070 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 55 GLN H 100 GLN H 112 HIS H 157 ASN J 17 ASN K 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 X 17 ASN X 22 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102168 restraints weight = 306165.214| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 5.53 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33510 Z= 0.128 Angle : 0.465 7.366 45269 Z= 0.264 Chirality : 0.038 0.157 4908 Planarity : 0.003 0.041 5822 Dihedral : 3.824 14.471 4332 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.35 % Allowed : 7.30 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 3992 helix: 1.30 (0.09), residues: 3128 sheet: None (None), residues: 0 loop : -2.14 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 180 HIS 0.008 0.001 HIS F 56 PHE 0.013 0.001 PHE S 131 TYR 0.016 0.001 TYR K 24 ARG 0.006 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 2517) hydrogen bonds : angle 3.52151 ( 7539) covalent geometry : bond 0.00228 (33510) covalent geometry : angle 0.46503 (45269) *********************** 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 569 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 551 time to evaluate : 3.753 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8700 (m-10) cc_final: 0.8463 (m-80) REVERT: B 167 LYS cc_start: 0.8368 (tttm) cc_final: 0.8139 (tttt) REVERT: B 169 MET cc_start: 0.8470 (ttm) cc_final: 0.8264 (mtp) REVERT: C 22 GLN cc_start: 0.8047 (tt0) cc_final: 0.7731 (mt0) REVERT: C 105 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7454 (mmp80) REVERT: D 47 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8555 (mtt) REVERT: D 148 ASP cc_start: 0.8352 (t0) cc_final: 0.8097 (t0) REVERT: D 169 MET cc_start: 0.8788 (ttm) cc_final: 0.8425 (ttm) REVERT: G 147 ASP cc_start: 0.8667 (t70) cc_final: 0.8421 (t70) REVERT: I 124 ASP cc_start: 0.8328 (m-30) cc_final: 0.8126 (t0) REVERT: I 143 LEU cc_start: 0.8671 (tp) cc_final: 0.8444 (tp) REVERT: K 16 ILE cc_start: 0.8239 (mm) cc_final: 0.7699 (mm) REVERT: K 105 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7970 (mmt90) REVERT: K 151 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7608 (mtmt) REVERT: M 55 GLN cc_start: 0.8144 (tp40) cc_final: 0.7938 (tp40) REVERT: M 135 TYR cc_start: 0.8596 (m-80) cc_final: 0.8364 (m-80) REVERT: M 167 LYS cc_start: 0.8973 (tttm) cc_final: 0.8765 (tttm) REVERT: O 67 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7344 (tm-30) REVERT: O 105 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7367 (mmp-170) REVERT: O 148 ASP cc_start: 0.8560 (m-30) cc_final: 0.8248 (m-30) REVERT: Q 25 LYS cc_start: 0.8066 (tttp) cc_final: 0.7706 (tttt) REVERT: Q 79 LYS cc_start: 0.7355 (pttm) cc_final: 0.7154 (mtpt) REVERT: Q 130 TYR cc_start: 0.8949 (t80) cc_final: 0.8737 (t80) REVERT: Q 147 ASP cc_start: 0.8475 (t70) cc_final: 0.8180 (t70) REVERT: R 42 ASP cc_start: 0.8488 (t0) cc_final: 0.8206 (t0) REVERT: S 55 GLN cc_start: 0.7973 (tp40) cc_final: 0.7661 (tp-100) REVERT: T 71 ASP cc_start: 0.8501 (t70) cc_final: 0.8282 (t0) REVERT: V 56 HIS cc_start: 0.7725 (t70) cc_final: 0.7415 (t70) REVERT: W 147 ASP cc_start: 0.8693 (t70) cc_final: 0.8347 (t0) REVERT: W 167 LYS cc_start: 0.7984 (tttm) cc_final: 0.7717 (ttpt) REVERT: W 169 MET cc_start: 0.8006 (ttm) cc_final: 0.7665 (ttm) REVERT: X 91 ILE cc_start: 0.9189 (mp) cc_final: 0.8973 (mp) REVERT: L 78 MET cc_start: 0.8434 (mtt) cc_final: 0.8075 (mtt) outliers start: 18 outliers final: 9 residues processed: 558 average time/residue: 0.4388 time to fit residues: 389.6744 Evaluate side-chains 457 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 447 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 MET 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 K residue 58 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 60 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 C 76 ASN E 17 ASN E 22 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 157 ASN J 17 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS U 76 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 22 GLN X 55 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101814 restraints weight = 343155.264| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 5.74 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1948 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= 0.127 Angle : 0.445 6.576 45269 Z= 0.254 Chirality : 0.038 0.186 4908 Planarity : 0.003 0.044 5822 Dihedral : 3.645 13.177 4330 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.71 % Allowed : 9.82 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 3992 helix: 1.85 (0.09), residues: 3130 sheet: None (None), residues: 0 loop : -1.81 (0.16), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 134 HIS 0.006 0.001 HIS R 56 PHE 0.011 0.001 PHE S 131 TYR 0.016 0.001 TYR K 24 ARG 0.007 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 2517) hydrogen bonds : angle 3.35517 ( 7539) covalent geometry : bond 0.00246 (33510) covalent geometry : angle 0.44461 (45269) *********************** 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 512 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 481 time to evaluate : 3.581 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8700 (m-10) cc_final: 0.8455 (m-80) REVERT: A 78 MET cc_start: 0.8925 (mtt) cc_final: 0.8611 (mtp) REVERT: B 167 LYS cc_start: 0.8404 (tttm) cc_final: 0.8173 (tttt) REVERT: C 22 GLN cc_start: 0.8060 (tt0) cc_final: 0.7742 (mt0) REVERT: C 78 MET cc_start: 0.8268 (mtt) cc_final: 0.7820 (mtt) REVERT: C 105 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7420 (mmp80) REVERT: E 169 MET cc_start: 0.8353 (ttm) cc_final: 0.7755 (mtm) REVERT: I 143 LEU cc_start: 0.8649 (tp) cc_final: 0.8448 (tp) REVERT: J 85 SER cc_start: 0.8943 (t) cc_final: 0.8094 (m) REVERT: J 169 MET cc_start: 0.7983 (ttm) cc_final: 0.7730 (ttm) REVERT: K 16 ILE cc_start: 0.8244 (mm) cc_final: 0.7696 (mm) REVERT: K 151 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7504 (mtmt) REVERT: M 135 TYR cc_start: 0.8649 (m-80) cc_final: 0.8418 (m-80) REVERT: O 105 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7309 (mmp-170) REVERT: O 148 ASP cc_start: 0.8496 (m-30) cc_final: 0.8206 (m-30) REVERT: Q 130 TYR cc_start: 0.8938 (t80) cc_final: 0.8726 (t80) REVERT: Q 147 ASP cc_start: 0.8403 (t70) cc_final: 0.8107 (t70) REVERT: R 42 ASP cc_start: 0.8432 (t0) cc_final: 0.8118 (t0) REVERT: S 47 MET cc_start: 0.8575 (mmm) cc_final: 0.8251 (mmm) REVERT: V 56 HIS cc_start: 0.7745 (t70) cc_final: 0.7499 (t70) REVERT: W 147 ASP cc_start: 0.8710 (t70) cc_final: 0.8287 (t0) REVERT: W 167 LYS cc_start: 0.8003 (tttm) cc_final: 0.7733 (ttpt) REVERT: W 169 MET cc_start: 0.8032 (ttm) cc_final: 0.7717 (ttm) REVERT: X 91 ILE cc_start: 0.9210 (mp) cc_final: 0.8987 (mp) REVERT: L 78 MET cc_start: 0.8293 (mtt) cc_final: 0.7913 (mtt) outliers start: 31 outliers final: 18 residues processed: 495 average time/residue: 0.4400 time to fit residues: 349.4115 Evaluate side-chains 462 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 444 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 90 SER Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain W residue 58 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 78 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 299 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 D 39 HIS E 17 ASN E 22 GLN F 17 ASN H 76 ASN H 157 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095850 restraints weight = 337394.045| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 5.71 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33510 Z= 0.192 Angle : 0.510 6.198 45269 Z= 0.288 Chirality : 0.040 0.192 4908 Planarity : 0.003 0.049 5822 Dihedral : 3.747 14.387 4330 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.22 % Allowed : 10.89 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.13), residues: 3992 helix: 1.84 (0.09), residues: 3133 sheet: None (None), residues: 0 loop : -1.73 (0.16), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 134 HIS 0.006 0.001 HIS F 56 PHE 0.014 0.001 PHE G 129 TYR 0.019 0.002 TYR M 24 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.07768 ( 2517) hydrogen bonds : angle 3.65929 ( 7539) covalent geometry : bond 0.00431 (33510) covalent geometry : angle 0.51033 (45269) *********************** 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 489 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 441 time to evaluate : 4.054 Fit side-chains REVERT: A 37 TYR cc_start: 0.8819 (m-10) cc_final: 0.8535 (m-80) REVERT: A 78 MET cc_start: 0.8915 (mtt) cc_final: 0.8610 (mtp) REVERT: B 167 LYS cc_start: 0.8421 (tttm) cc_final: 0.8181 (tttt) REVERT: C 105 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7505 (mmp80) REVERT: G 125 ASP cc_start: 0.7794 (t0) cc_final: 0.7422 (t70) REVERT: I 22 GLN cc_start: 0.7861 (tt0) cc_final: 0.7522 (mt0) REVERT: I 143 LEU cc_start: 0.8772 (tp) cc_final: 0.8570 (tp) REVERT: K 16 ILE cc_start: 0.8412 (mm) cc_final: 0.7769 (mm) REVERT: K 151 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7580 (mtmt) REVERT: M 151 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7922 (ptpp) REVERT: N 103 TYR cc_start: 0.8568 (t80) cc_final: 0.8343 (t80) REVERT: O 105 ARG cc_start: 0.7690 (mmt90) cc_final: 0.7419 (mmp-170) REVERT: O 148 ASP cc_start: 0.8529 (m-30) cc_final: 0.8196 (m-30) REVERT: R 42 ASP cc_start: 0.8532 (t0) cc_final: 0.8267 (t0) REVERT: R 101 GLU cc_start: 0.7584 (tt0) cc_final: 0.7329 (tt0) REVERT: T 22 GLN cc_start: 0.7909 (tp40) cc_final: 0.7553 (tm-30) REVERT: W 167 LYS cc_start: 0.8070 (tttm) cc_final: 0.7810 (ttpt) REVERT: W 169 MET cc_start: 0.8205 (ttm) cc_final: 0.7867 (ttm) REVERT: L 78 MET cc_start: 0.8382 (mtt) cc_final: 0.7922 (mtt) outliers start: 48 outliers final: 39 residues processed: 468 average time/residue: 0.4285 time to fit residues: 324.4583 Evaluate side-chains 457 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 418 time to evaluate : 3.451 ------------------------------------------------------------------------------- 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 17 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain 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 91 ILE 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 91 ILE Chi-restraints excluded: chain Q residue 93 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 124 ASP Chi-restraints excluded: chain S residue 144 THR 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 V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 76 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 172 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 369 optimal weight: 8.9990 chunk 383 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 100 GLN D 154 ASN E 17 ASN E 22 GLN H 76 ASN H 157 ASN J 23 HIS J 27 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095906 restraints weight = 321387.819| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 5.59 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33510 Z= 0.187 Angle : 0.501 6.419 45269 Z= 0.283 Chirality : 0.040 0.169 4908 Planarity : 0.003 0.047 5822 Dihedral : 3.759 14.823 4330 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.19 % Allowed : 11.50 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.13), residues: 3992 helix: 1.92 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.63 (0.16), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 134 HIS 0.005 0.001 HIS V 39 PHE 0.013 0.001 PHE N 131 TYR 0.017 0.002 TYR M 24 ARG 0.007 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.07678 ( 2517) hydrogen bonds : angle 3.64921 ( 7539) covalent geometry : bond 0.00415 (33510) covalent geometry : angle 0.50088 (45269) *********************** 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 473 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 425 time to evaluate : 3.661 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8794 (m-10) cc_final: 0.8509 (m-80) REVERT: A 78 MET cc_start: 0.8981 (mtt) cc_final: 0.8669 (mtp) REVERT: B 167 LYS cc_start: 0.8412 (tttm) cc_final: 0.8175 (tttt) REVERT: C 22 GLN cc_start: 0.8269 (tt0) cc_final: 0.7903 (mt0) REVERT: C 105 ARG cc_start: 0.8050 (mmt90) cc_final: 0.7519 (mmp80) REVERT: G 125 ASP cc_start: 0.7758 (t0) cc_final: 0.7358 (t70) REVERT: I 22 GLN cc_start: 0.7874 (tt0) cc_final: 0.7534 (mt0) REVERT: I 24 TYR cc_start: 0.8983 (t80) cc_final: 0.8542 (t80) REVERT: K 16 ILE cc_start: 0.8384 (mm) cc_final: 0.7775 (mm) REVERT: K 151 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7618 (mtmt) REVERT: M 47 MET cc_start: 0.9056 (mtp) cc_final: 0.8691 (mtp) REVERT: N 47 MET cc_start: 0.8740 (mmt) cc_final: 0.8477 (tpp) REVERT: N 103 TYR cc_start: 0.8633 (t80) cc_final: 0.8388 (t80) REVERT: O 105 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7420 (mmp-170) REVERT: O 148 ASP cc_start: 0.8568 (m-30) cc_final: 0.8242 (m-30) REVERT: Q 100 GLN cc_start: 0.7893 (mt0) cc_final: 0.7645 (mt0) REVERT: R 42 ASP cc_start: 0.8538 (t0) cc_final: 0.8273 (t0) REVERT: R 101 GLU cc_start: 0.7592 (tt0) cc_final: 0.7343 (tt0) REVERT: W 167 LYS cc_start: 0.7992 (tttm) cc_final: 0.7718 (ttpt) REVERT: W 169 MET cc_start: 0.8085 (ttm) cc_final: 0.7736 (ttm) REVERT: L 78 MET cc_start: 0.8386 (mtt) cc_final: 0.7935 (mtt) outliers start: 48 outliers final: 39 residues processed: 454 average time/residue: 0.4475 time to fit residues: 329.9584 Evaluate side-chains 451 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 412 time to evaluate : 3.867 ------------------------------------------------------------------------------- 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 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 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 91 ILE 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 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 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 124 ASP Chi-restraints excluded: chain S residue 144 THR 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 V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 81 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 100 GLN E 17 ASN E 22 GLN H 157 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096233 restraints weight = 342060.564| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.77 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33510 Z= 0.180 Angle : 0.493 6.590 45269 Z= 0.280 Chirality : 0.039 0.169 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.746 14.800 4330 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.22 % Allowed : 11.84 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.13), residues: 3992 helix: 2.00 (0.09), residues: 3131 sheet: None (None), residues: 0 loop : -1.52 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 134 HIS 0.005 0.001 HIS V 39 PHE 0.012 0.001 PHE N 131 TYR 0.017 0.002 TYR M 24 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.07565 ( 2517) hydrogen bonds : angle 3.61418 ( 7539) covalent geometry : bond 0.00397 (33510) covalent geometry : angle 0.49311 (45269) *********************** 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 477 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 429 time to evaluate : 3.610 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8790 (m-10) cc_final: 0.8516 (m-80) REVERT: A 78 MET cc_start: 0.8991 (mtt) cc_final: 0.8677 (mtp) REVERT: B 167 LYS cc_start: 0.8404 (tttm) cc_final: 0.8156 (tttt) REVERT: C 22 GLN cc_start: 0.8260 (tt0) cc_final: 0.7898 (mt0) REVERT: C 105 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7533 (mmp80) REVERT: G 125 ASP cc_start: 0.7760 (t0) cc_final: 0.7332 (t70) REVERT: I 22 GLN cc_start: 0.7864 (tt0) cc_final: 0.7516 (mt0) REVERT: K 16 ILE cc_start: 0.8321 (mm) cc_final: 0.7727 (mm) REVERT: K 151 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7639 (mtmt) REVERT: N 103 TYR cc_start: 0.8626 (t80) cc_final: 0.8379 (t80) REVERT: O 105 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7421 (mmp-170) REVERT: O 148 ASP cc_start: 0.8586 (m-30) cc_final: 0.8232 (m-30) REVERT: Q 100 GLN cc_start: 0.7907 (mt0) cc_final: 0.7672 (mt0) REVERT: Q 158 ASP cc_start: 0.7596 (m-30) cc_final: 0.7185 (m-30) REVERT: R 42 ASP cc_start: 0.8541 (t0) cc_final: 0.8279 (t0) REVERT: R 101 GLU cc_start: 0.7565 (tt0) cc_final: 0.7073 (tt0) REVERT: R 105 ARG cc_start: 0.8338 (mmt90) cc_final: 0.7869 (mmt90) REVERT: W 167 LYS cc_start: 0.7992 (tttm) cc_final: 0.7714 (ttpt) REVERT: W 169 MET cc_start: 0.8073 (ttm) cc_final: 0.7741 (ttm) REVERT: L 78 MET cc_start: 0.8379 (mtt) cc_final: 0.7946 (mtt) outliers start: 48 outliers final: 45 residues processed: 456 average time/residue: 0.4351 time to fit residues: 320.4539 Evaluate side-chains 456 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 411 time to evaluate : 3.470 ------------------------------------------------------------------------------- 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 57 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 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 91 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 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 P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 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 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 45 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 H 17 ASN H 157 ASN J 27 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102253 restraints weight = 349219.168| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.84 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 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 = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33510 Z= 0.120 Angle : 0.436 6.859 45269 Z= 0.248 Chirality : 0.037 0.177 4908 Planarity : 0.003 0.044 5822 Dihedral : 3.604 15.717 4330 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.71 % Allowed : 12.60 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.13), residues: 3992 helix: 2.37 (0.09), residues: 3130 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 134 HIS 0.005 0.001 HIS S 39 PHE 0.010 0.001 PHE S 131 TYR 0.016 0.001 TYR K 24 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.05599 ( 2517) hydrogen bonds : angle 3.22798 ( 7539) covalent geometry : bond 0.00227 (33510) covalent geometry : angle 0.43561 (45269) *********************** 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 486 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 457 time to evaluate : 3.517 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8693 (m-10) cc_final: 0.8451 (m-80) REVERT: A 78 MET cc_start: 0.8998 (mtt) cc_final: 0.8754 (mtp) REVERT: B 167 LYS cc_start: 0.8406 (tttm) cc_final: 0.8158 (tttt) REVERT: C 22 GLN cc_start: 0.8132 (tt0) cc_final: 0.7838 (mt0) REVERT: C 105 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7433 (mmp80) REVERT: G 125 ASP cc_start: 0.7589 (t0) cc_final: 0.7224 (t70) REVERT: I 43 ASP cc_start: 0.8029 (p0) cc_final: 0.7706 (t70) REVERT: I 78 MET cc_start: 0.8284 (mtt) cc_final: 0.8053 (mtt) REVERT: J 85 SER cc_start: 0.8946 (t) cc_final: 0.8113 (m) REVERT: K 16 ILE cc_start: 0.8075 (mm) cc_final: 0.7524 (mm) REVERT: K 151 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7388 (mttt) REVERT: M 135 TYR cc_start: 0.8632 (m-80) cc_final: 0.8411 (m-80) REVERT: M 144 THR cc_start: 0.8822 (t) cc_final: 0.8592 (m) REVERT: N 106 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8060 (mm-30) REVERT: N 119 LEU cc_start: 0.8373 (tp) cc_final: 0.8155 (tp) REVERT: O 105 ARG cc_start: 0.7623 (mmt90) cc_final: 0.7373 (mmp80) REVERT: O 148 ASP cc_start: 0.8530 (m-30) cc_final: 0.8149 (m-30) REVERT: Q 158 ASP cc_start: 0.7614 (m-30) cc_final: 0.7207 (m-30) REVERT: R 42 ASP cc_start: 0.8427 (t0) cc_final: 0.8193 (t0) REVERT: S 47 MET cc_start: 0.8638 (mmm) cc_final: 0.7814 (mmt) REVERT: W 163 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8099 (mm-30) REVERT: W 167 LYS cc_start: 0.8012 (tttm) cc_final: 0.7706 (ttpt) REVERT: W 169 MET cc_start: 0.7934 (ttm) cc_final: 0.7722 (ttm) REVERT: L 78 MET cc_start: 0.8251 (mtt) cc_final: 0.7920 (mtt) outliers start: 29 outliers final: 24 residues processed: 472 average time/residue: 0.4260 time to fit residues: 326.4338 Evaluate side-chains 447 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 423 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 93 SER 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 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain 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 113 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 308 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 356 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 H 157 ASN J 17 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 HIS M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096830 restraints weight = 357810.876| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.88 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33510 Z= 0.179 Angle : 0.493 8.396 45269 Z= 0.279 Chirality : 0.039 0.183 4908 Planarity : 0.003 0.047 5822 Dihedral : 3.674 14.209 4330 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.10 % Allowed : 12.96 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.13), residues: 3992 helix: 2.22 (0.09), residues: 3142 sheet: None (None), residues: 0 loop : -1.38 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 134 HIS 0.008 0.001 HIS R 56 PHE 0.012 0.001 PHE G 129 TYR 0.018 0.002 TYR M 24 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.07276 ( 2517) hydrogen bonds : angle 3.52263 ( 7539) covalent geometry : bond 0.00396 (33510) covalent geometry : angle 0.49263 (45269) *********************** 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 462 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 419 time to evaluate : 4.017 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8798 (m-10) cc_final: 0.8523 (m-80) REVERT: A 78 MET cc_start: 0.9013 (mtt) cc_final: 0.8659 (mtp) REVERT: A 107 ASN cc_start: 0.8780 (t0) cc_final: 0.8501 (m-40) REVERT: B 167 LYS cc_start: 0.8406 (tttm) cc_final: 0.8149 (tttt) REVERT: C 22 GLN cc_start: 0.8263 (tt0) cc_final: 0.7924 (mt0) REVERT: C 105 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7505 (mmp80) REVERT: G 125 ASP cc_start: 0.7871 (t0) cc_final: 0.7438 (t70) REVERT: I 22 GLN cc_start: 0.7827 (tt0) cc_final: 0.7494 (mt0) REVERT: I 43 ASP cc_start: 0.8033 (p0) cc_final: 0.7605 (t70) REVERT: J 85 SER cc_start: 0.8979 (t) cc_final: 0.8183 (m) REVERT: K 16 ILE cc_start: 0.8284 (mm) cc_final: 0.7698 (mm) REVERT: K 151 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7605 (mtmt) REVERT: N 47 MET cc_start: 0.8682 (mmt) cc_final: 0.8328 (mmt) REVERT: O 148 ASP cc_start: 0.8568 (m-30) cc_final: 0.8182 (m-30) REVERT: Q 158 ASP cc_start: 0.7605 (m-30) cc_final: 0.7195 (m-30) REVERT: R 42 ASP cc_start: 0.8504 (t0) cc_final: 0.8239 (t0) REVERT: W 167 LYS cc_start: 0.8064 (tttm) cc_final: 0.7791 (ttpt) REVERT: W 169 MET cc_start: 0.8064 (ttm) cc_final: 0.7745 (ttm) REVERT: L 78 MET cc_start: 0.8336 (mtt) cc_final: 0.7902 (mtt) outliers start: 43 outliers final: 39 residues processed: 441 average time/residue: 0.4334 time to fit residues: 310.4903 Evaluate side-chains 445 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 406 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 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 P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 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 V residue 169 MET Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 111 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 362 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 H 157 ASN J 17 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099480 restraints weight = 334899.265| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.76 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33510 Z= 0.136 Angle : 0.452 8.538 45269 Z= 0.257 Chirality : 0.038 0.177 4908 Planarity : 0.003 0.045 5822 Dihedral : 3.616 15.183 4330 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.99 % Allowed : 12.96 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.13), residues: 3992 helix: 2.37 (0.09), residues: 3141 sheet: None (None), residues: 0 loop : -1.29 (0.17), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 PHE 0.010 0.001 PHE T 129 TYR 0.019 0.001 TYR N 103 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 2517) hydrogen bonds : angle 3.33721 ( 7539) covalent geometry : bond 0.00274 (33510) covalent geometry : angle 0.45242 (45269) *********************** 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 464 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 425 time to evaluate : 4.015 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8730 (m-10) cc_final: 0.8452 (m-80) REVERT: A 78 MET cc_start: 0.9006 (mtt) cc_final: 0.8682 (mtp) REVERT: A 107 ASN cc_start: 0.8761 (t0) cc_final: 0.8492 (m-40) REVERT: B 167 LYS cc_start: 0.8363 (tttm) cc_final: 0.8116 (tttt) REVERT: C 22 GLN cc_start: 0.8166 (tt0) cc_final: 0.7854 (mt0) REVERT: C 105 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7467 (mmp80) REVERT: G 125 ASP cc_start: 0.7728 (t0) cc_final: 0.7308 (t70) REVERT: I 22 GLN cc_start: 0.7779 (tt0) cc_final: 0.7484 (mt0) REVERT: I 43 ASP cc_start: 0.8054 (p0) cc_final: 0.7558 (t70) REVERT: I 78 MET cc_start: 0.8361 (mtt) cc_final: 0.8153 (mtt) REVERT: I 137 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8239 (ttp80) REVERT: J 85 SER cc_start: 0.9029 (t) cc_final: 0.8206 (m) REVERT: K 16 ILE cc_start: 0.8165 (mm) cc_final: 0.7585 (mm) REVERT: K 151 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7405 (mttt) REVERT: N 106 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8114 (mm-30) REVERT: O 148 ASP cc_start: 0.8532 (m-30) cc_final: 0.8132 (m-30) REVERT: Q 158 ASP cc_start: 0.7617 (m-30) cc_final: 0.7229 (m-30) REVERT: R 42 ASP cc_start: 0.8429 (t0) cc_final: 0.8189 (t0) REVERT: R 59 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8020 (tp30) REVERT: W 163 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8136 (mm-30) REVERT: W 167 LYS cc_start: 0.8009 (tttm) cc_final: 0.7706 (ttpt) REVERT: W 169 MET cc_start: 0.7961 (ttm) cc_final: 0.7732 (ttm) REVERT: L 78 MET cc_start: 0.8318 (mtt) cc_final: 0.7908 (mtt) outliers start: 39 outliers final: 36 residues processed: 447 average time/residue: 0.4312 time to fit residues: 314.7534 Evaluate side-chains 450 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 414 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 107 ASN 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 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 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 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain L residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 227 optimal weight: 0.0970 chunk 164 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 H 157 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS 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 = 0.3538 r_free = 0.3538 target = 0.115745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098512 restraints weight = 338783.715| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.77 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 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 = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33510 Z= 0.153 Angle : 0.470 8.441 45269 Z= 0.266 Chirality : 0.039 0.225 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.627 15.727 4330 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.94 % Allowed : 13.05 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.13), residues: 3992 helix: 2.34 (0.09), residues: 3141 sheet: None (None), residues: 0 loop : -1.28 (0.17), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 PHE 0.011 0.001 PHE T 129 TYR 0.018 0.001 TYR N 103 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.06647 ( 2517) hydrogen bonds : angle 3.40400 ( 7539) covalent geometry : bond 0.00325 (33510) covalent geometry : angle 0.46976 (45269) ********************** 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 452 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 415 time to evaluate : 3.780 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8759 (m-10) cc_final: 0.8486 (m-80) REVERT: A 78 MET cc_start: 0.9016 (mtt) cc_final: 0.8679 (mtp) REVERT: A 107 ASN cc_start: 0.8776 (t0) cc_final: 0.8516 (m-40) REVERT: B 167 LYS cc_start: 0.8381 (tttm) cc_final: 0.8131 (tttt) REVERT: C 22 GLN cc_start: 0.8201 (tt0) cc_final: 0.7877 (mt0) REVERT: C 105 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7485 (mmp80) REVERT: G 125 ASP cc_start: 0.7761 (t0) cc_final: 0.7345 (t70) REVERT: I 22 GLN cc_start: 0.7797 (tt0) cc_final: 0.7498 (mt0) REVERT: I 43 ASP cc_start: 0.8062 (p0) cc_final: 0.7552 (t70) REVERT: I 137 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8238 (ttp80) REVERT: J 85 SER cc_start: 0.9060 (t) cc_final: 0.8224 (m) REVERT: K 16 ILE cc_start: 0.8198 (mm) cc_final: 0.7621 (mm) REVERT: K 151 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7634 (mtmt) REVERT: N 106 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8126 (mm-30) REVERT: O 148 ASP cc_start: 0.8525 (m-30) cc_final: 0.8125 (m-30) REVERT: Q 158 ASP cc_start: 0.7576 (m-30) cc_final: 0.7176 (m-30) REVERT: R 42 ASP cc_start: 0.8432 (t0) cc_final: 0.8188 (t0) REVERT: R 59 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8015 (tp30) REVERT: W 163 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8244 (mm-30) REVERT: W 167 LYS cc_start: 0.7989 (tttm) cc_final: 0.7695 (ttpt) REVERT: W 169 MET cc_start: 0.7974 (ttm) cc_final: 0.7736 (ttm) REVERT: L 78 MET cc_start: 0.8342 (mtt) cc_final: 0.7929 (mtt) outliers start: 37 outliers final: 35 residues processed: 436 average time/residue: 0.4295 time to fit residues: 304.4878 Evaluate side-chains 446 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 411 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain F residue 107 ASN 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 58 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 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 76 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 344 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 285 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 H 14 ASN H 157 ASN J 17 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS R 56 HIS ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098665 restraints weight = 352863.874| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.88 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 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 = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33510 Z= 0.146 Angle : 0.464 8.423 45269 Z= 0.263 Chirality : 0.038 0.210 4908 Planarity : 0.003 0.046 5822 Dihedral : 3.627 18.717 4330 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.13), residues: 3992 helix: 2.37 (0.09), residues: 3141 sheet: None (None), residues: 0 loop : -1.25 (0.17), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 134 HIS 0.008 0.001 HIS R 56 PHE 0.011 0.001 PHE T 129 TYR 0.018 0.001 TYR N 103 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.06558 ( 2517) hydrogen bonds : angle 3.38767 ( 7539) covalent geometry : bond 0.00303 (33510) covalent geometry : angle 0.46382 (45269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12691.40 seconds wall clock time: 221 minutes 48.58 seconds (13308.58 seconds total)