Starting phenix.real_space_refine on Sat Jun 28 01:05:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqy_37758/06_2025/8wqy_37758.cif" } resolution = 3.0 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= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20998 2.51 5 N 5346 2.21 5 O 6420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32860 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "D" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "E" Number of atoms: 1364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1346 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 164, 1346 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 2 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "G" Number of atoms: 1362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1350 Chain: "H" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "I" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1360 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1360 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1367 Chain: "J" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "K" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "L" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "M" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "N" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "O" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "P" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "Q" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "R" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "S" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "T" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "U" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "V" Number of atoms: 1381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1370 Chain: "W" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "X" Number of atoms: 1381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 166, 1363 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 bond proxies already assigned to first conformer: 1370 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: "L" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 31.85, per 1000 atoms: 0.97 Number of scatterers: 32860 At special positions: 0 Unit cell: (146.566, 145.519, 149.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 72 16.00 O 6420 8.00 N 5346 7.00 C 20998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 7.6 seconds 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7706 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 12 sheets defined 83.3% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 44 Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.963A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 123 removed outlier: 3.708A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 3.785A pdb=" N PHE A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.895A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 45 removed outlier: 3.589A pdb=" N PHE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.640A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 122 removed outlier: 3.702A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.363A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.942A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 45 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.698A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 122 removed outlier: 3.523A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.708A pdb=" N PHE C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.576A pdb=" N PHE D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.386A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 122 removed outlier: 3.849A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.810A pdb=" N PHE D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.771A pdb=" N ILE D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.900A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.591A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.884A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 155 removed outlier: 3.903A pdb=" N PHE E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 155 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 removed outlier: 3.516A pdb=" N PHE F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.482A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.949A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 3.582A pdb=" N PHE F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 removed outlier: 3.984A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 156' Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.974A pdb=" N ILE F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 44 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.161A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 122 removed outlier: 3.601A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 3.652A pdb=" N PHE G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 156 removed outlier: 3.929A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 151 through 156' Processing helix chain 'G' and resid 158 through 172 removed outlier: 3.608A pdb=" N ILE G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 45 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.842A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 3.567A pdb=" N PHE H 129 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 removed outlier: 3.677A pdb=" N ILE H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 44 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.507A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.656A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 4.639A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 removed outlier: 4.249A pdb=" N ILE I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 45 removed outlier: 3.667A pdb=" N PHE J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.664A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.520A pdb=" N LEU J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 151 removed outlier: 4.562A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 44 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.848A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.551A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 3.516A pdb=" N PHE K 129 " --> pdb=" O ASP K 125 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 removed outlier: 3.519A pdb=" N ILE K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 44 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.387A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.739A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 3.660A pdb=" N PHE L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 removed outlier: 4.180A pdb=" N ILE L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 44 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.172A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 122 removed outlier: 3.618A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 removed outlier: 3.750A pdb=" N ILE M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 151 removed outlier: 3.944A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 removed outlier: 3.684A pdb=" N ILE M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 45 removed outlier: 3.517A pdb=" N PHE N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.642A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.816A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 3.625A pdb=" N PHE N 129 " --> pdb=" O ASP N 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 170 Processing helix chain 'O' and resid 14 through 44 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.575A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.583A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 3.666A pdb=" N PHE O 129 " --> pdb=" O ASP O 125 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 44 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.474A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.533A pdb=" N LEU P 98 " --> pdb=" O ASP P 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 3.740A pdb=" N PHE P 129 " --> pdb=" O ASP P 125 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 171 removed outlier: 3.664A pdb=" N ILE P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 45 removed outlier: 3.626A pdb=" N PHE Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.484A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 122 Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.428A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 removed outlier: 3.730A pdb=" N PHE R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.508A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.714A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.373A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 172 removed outlier: 3.709A pdb=" N ILE R 162 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS R 172 " --> pdb=" O GLU R 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 44 Processing helix chain 'S' and resid 47 through 63 removed outlier: 3.507A pdb=" N GLY S 51 " --> pdb=" O MET S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.437A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.617A pdb=" N LEU S 98 " --> pdb=" O ASP S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.927A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 44 removed outlier: 3.524A pdb=" N HIS T 36 " --> pdb=" O LEU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.499A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.524A pdb=" N VAL T 109 " --> pdb=" O ARG T 105 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG T 110 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU T 123 " --> pdb=" O LEU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 3.592A pdb=" N PHE T 129 " --> pdb=" O ASP T 125 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 removed outlier: 3.575A pdb=" N SER T 155 " --> pdb=" O LEU T 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 152 through 155' Processing helix chain 'T' and resid 158 through 171 removed outlier: 3.646A pdb=" N ILE T 162 " --> pdb=" O ASP T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 45 removed outlier: 3.576A pdb=" N PHE U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 5.062A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.551A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 3.749A pdb=" N PHE U 129 " --> pdb=" O ASP U 125 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 44 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.285A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.670A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 3.966A pdb=" N PHE V 129 " --> pdb=" O ASP V 125 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 172 removed outlier: 3.863A pdb=" N ILE V 162 " --> pdb=" O ASP V 158 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS V 172 " --> pdb=" O GLU V 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 45 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.767A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 123 removed outlier: 3.562A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 3.583A pdb=" N PHE W 129 " --> pdb=" O ASP W 125 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 171 removed outlier: 3.589A pdb=" N ILE W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 44 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.661A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.661A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU X 123 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.572A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2573 hydrogen bonds defined for protein. 7701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.53 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5888 1.30 - 1.43: 8627 1.43 - 1.55: 18861 1.55 - 1.68: 0 1.68 - 1.80: 144 Bond restraints: 33520 Sorted by residual: bond pdb=" CA ASP V 125 " pdb=" C ASP V 125 " ideal model delta sigma weight residual 1.521 1.437 0.085 1.17e-02 7.31e+03 5.22e+01 bond pdb=" CA GLN E 133 " pdb=" C GLN E 133 " ideal model delta sigma weight residual 1.525 1.453 0.072 1.38e-02 5.25e+03 2.73e+01 bond pdb=" CA TRP E 134 " pdb=" C TRP E 134 " ideal model delta sigma weight residual 1.519 1.459 0.060 1.22e-02 6.72e+03 2.40e+01 bond pdb=" CA ASP T 125 " pdb=" C ASP T 125 " ideal model delta sigma weight residual 1.526 1.465 0.062 1.35e-02 5.49e+03 2.08e+01 bond pdb=" CA HIS T 36 " pdb=" C HIS T 36 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.37e-02 5.33e+03 1.97e+01 ... (remaining 33515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 45128 3.11 - 6.22: 146 6.22 - 9.33: 6 9.33 - 12.45: 3 12.45 - 15.56: 1 Bond angle restraints: 45284 Sorted by residual: angle pdb=" N TRP E 134 " pdb=" CA TRP E 134 " pdb=" C TRP E 134 " ideal model delta sigma weight residual 113.55 97.99 15.56 1.26e+00 6.30e-01 1.52e+02 angle pdb=" N HIS T 36 " pdb=" CA HIS T 36 " pdb=" C HIS T 36 " ideal model delta sigma weight residual 112.45 100.82 11.63 1.39e+00 5.18e-01 7.00e+01 angle pdb=" N PHE M 129 " pdb=" CA PHE M 129 " pdb=" C PHE M 129 " ideal model delta sigma weight residual 113.97 105.18 8.79 1.28e+00 6.10e-01 4.72e+01 angle pdb=" N VAL T 109 " pdb=" CA VAL T 109 " pdb=" C VAL T 109 " ideal model delta sigma weight residual 110.53 104.14 6.39 9.40e-01 1.13e+00 4.62e+01 angle pdb=" N ASN T 107 " pdb=" CA ASN T 107 " pdb=" C ASN T 107 " ideal model delta sigma weight residual 113.72 105.10 8.62 1.30e+00 5.92e-01 4.40e+01 ... (remaining 45279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 18157 18.06 - 36.12: 1586 36.12 - 54.17: 255 54.17 - 72.23: 81 72.23 - 90.29: 45 Dihedral angle restraints: 20124 sinusoidal: 8182 harmonic: 11942 Sorted by residual: dihedral pdb=" C ASP V 125 " pdb=" N ASP V 125 " pdb=" CA ASP V 125 " pdb=" CB ASP V 125 " ideal model delta harmonic sigma weight residual -122.60 -110.05 -12.55 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" C TYR T 126 " pdb=" N TYR T 126 " pdb=" CA TYR T 126 " pdb=" CB TYR T 126 " ideal model delta harmonic sigma weight residual -122.60 -133.20 10.60 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C ASP T 125 " pdb=" N ASP T 125 " pdb=" CA ASP T 125 " pdb=" CB ASP T 125 " ideal model delta harmonic sigma weight residual -122.60 -112.61 -9.99 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 20121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4808 0.105 - 0.210: 92 0.210 - 0.315: 4 0.315 - 0.420: 4 0.420 - 0.525: 1 Chirality restraints: 4909 Sorted by residual: chirality pdb=" CA TYR T 126 " pdb=" N TYR T 126 " pdb=" C TYR T 126 " pdb=" CB TYR T 126 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA TYR M 126 " pdb=" N TYR M 126 " pdb=" C TYR M 126 " pdb=" CB TYR M 126 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASP V 124 " pdb=" N ASP V 124 " pdb=" C ASP V 124 " pdb=" CB ASP V 124 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4906 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AGLU T 108 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C AGLU T 108 " 0.070 2.00e-02 2.50e+03 pdb=" O AGLU T 108 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL T 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 99 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C ILE T 99 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE T 99 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN T 100 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS T 25 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LYS T 25 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS T 25 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU T 26 " -0.013 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 138 2.49 - 3.10: 22987 3.10 - 3.70: 47868 3.70 - 4.30: 69069 4.30 - 4.90: 118175 Nonbonded interactions: 258237 Sorted by model distance: nonbonded pdb=" OD2 ASP V 138 " pdb="FE FE V 201 " model vdw 1.893 2.260 nonbonded pdb=" OD2 ASP O 138 " pdb="FE FE O 201 " model vdw 1.930 2.260 nonbonded pdb=" OD2 ASP G 142 " pdb="FE FE G 201 " model vdw 1.935 2.260 nonbonded pdb="FE FE F 201 " pdb=" O HOH F 302 " model vdw 1.958 2.260 nonbonded pdb=" OD2 ASP G 138 " pdb="FE FE G 201 " model vdw 1.964 2.260 ... (remaining 258232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 176 or resid 178 through 181)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 147 or resid 149 through 171 or resid 178 through 181)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 1.380 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 85.950 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.220 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33520 Z= 0.302 Angle : 0.593 15.556 45284 Z= 0.364 Chirality : 0.044 0.525 4909 Planarity : 0.003 0.047 5825 Dihedral : 14.605 90.291 12418 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.01 % Allowed : 2.66 % Favored : 96.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.11), residues: 3995 helix: 0.00 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.76 (0.13), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 134 HIS 0.007 0.001 HIS W 23 PHE 0.014 0.002 PHE A 129 TYR 0.019 0.002 TYR A 37 ARG 0.006 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.13373 ( 2573) hydrogen bonds : angle 4.73876 ( 7701) covalent geometry : bond 0.00591 (33520) covalent geometry : angle 0.59294 (45284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 541 time to evaluate : 3.691 Fit side-chains REVERT: A 114 LYS cc_start: 0.7220 (ttmt) cc_final: 0.7019 (tttp) REVERT: A 141 LYS cc_start: 0.7960 (tttt) cc_final: 0.7397 (ttpt) REVERT: B 107 ASN cc_start: 0.8885 (t0) cc_final: 0.8488 (m-40) REVERT: C 111 ASP cc_start: 0.7803 (t0) cc_final: 0.7442 (t0) REVERT: D 163 GLU cc_start: 0.7696 (mp0) cc_final: 0.7235 (mp0) REVERT: E 29 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7997 (mt-10) REVERT: F 67 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 59 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6938 (mt-10) REVERT: G 67 GLU cc_start: 0.7471 (tp30) cc_final: 0.7203 (mm-30) REVERT: G 105 ARG cc_start: 0.7554 (mmt90) cc_final: 0.7083 (mmp80) REVERT: G 157 ASN cc_start: 0.7722 (p0) cc_final: 0.7450 (m-40) REVERT: H 85 SER cc_start: 0.8902 (p) cc_final: 0.8635 (t) REVERT: H 125 ASP cc_start: 0.8169 (t70) cc_final: 0.7907 (t0) REVERT: I 22 GLN cc_start: 0.7511 (mm110) cc_final: 0.7056 (mt0) REVERT: I 81 LYS cc_start: 0.7748 (mttt) cc_final: 0.7424 (mmtp) REVERT: J 22 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7675 (mm-40) REVERT: K 56 HIS cc_start: 0.7162 (m-70) cc_final: 0.6684 (t70) REVERT: M 67 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7741 (mp0) REVERT: M 101 GLU cc_start: 0.7125 (tp30) cc_final: 0.6777 (mm-30) REVERT: N 125 ASP cc_start: 0.8630 (t70) cc_final: 0.8366 (t0) REVERT: O 22 GLN cc_start: 0.8039 (tp40) cc_final: 0.7798 (mm-40) REVERT: O 105 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7240 (mmp80) REVERT: P 22 GLN cc_start: 0.7873 (mm110) cc_final: 0.7642 (mt0) REVERT: P 71 ASP cc_start: 0.8166 (t0) cc_final: 0.7850 (t0) REVERT: Q 22 GLN cc_start: 0.8068 (mm110) cc_final: 0.7728 (tt0) REVERT: Q 148 ASP cc_start: 0.8274 (t0) cc_final: 0.8006 (t0) REVERT: R 137 ARG cc_start: 0.8234 (ttp80) cc_final: 0.8031 (ttm170) REVERT: S 56 HIS cc_start: 0.7599 (m-70) cc_final: 0.7173 (t-90) REVERT: S 148 ASP cc_start: 0.7811 (m-30) cc_final: 0.7321 (m-30) REVERT: T 78 MET cc_start: 0.8081 (mtt) cc_final: 0.7762 (mtt) REVERT: T 105 ARG cc_start: 0.7565 (mmt90) cc_final: 0.6911 (mtp85) REVERT: T 106 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8448 (tp30) REVERT: T 148 ASP cc_start: 0.7889 (t0) cc_final: 0.7664 (t0) REVERT: V 14 ASN cc_start: 0.7137 (t0) cc_final: 0.6445 (t0) REVERT: V 18 ASP cc_start: 0.7667 (m-30) cc_final: 0.7325 (m-30) REVERT: W 47 MET cc_start: 0.9028 (mtp) cc_final: 0.8752 (mtt) REVERT: W 56 HIS cc_start: 0.7972 (m-70) cc_final: 0.7747 (m90) REVERT: X 56 HIS cc_start: 0.7223 (t-90) cc_final: 0.6486 (t-90) outliers start: 4 outliers final: 3 residues processed: 544 average time/residue: 1.4035 time to fit residues: 907.4743 Evaluate side-chains 344 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 341 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain M residue 127 GLU Chi-restraints excluded: chain S residue 111 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9990 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 2.9990 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 154 ASN B 17 ASN C 22 GLN C 154 ASN D 17 ASN D 55 GLN D 65 HIS D 154 ASN E 17 ASN F 107 ASN G 22 GLN G 154 ASN H 39 HIS J 36 HIS J 154 ASN K 17 ASN K 65 HIS K 76 ASN K 177 HIS M 17 ASN N 154 ASN O 17 ASN P 17 ASN P 56 HIS P 76 ASN Q 22 GLN Q 36 HIS Q 56 HIS Q 100 GLN R 23 HIS R 39 HIS R 154 ASN S 154 ASN T 14 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 154 ASN U 14 ASN U 39 HIS V 17 ASN V 100 GLN W 154 ASN X 17 ASN X 100 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100808 restraints weight = 299823.446| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 5.15 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33520 Z= 0.142 Angle : 0.479 7.741 45284 Z= 0.273 Chirality : 0.038 0.185 4909 Planarity : 0.003 0.041 5825 Dihedral : 3.983 60.838 4339 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.82 % Allowed : 9.79 % Favored : 88.39 % 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: 1.20 (0.13), residues: 3995 helix: 1.55 (0.09), residues: 3118 sheet: None (None), residues: 0 loop : -1.99 (0.16), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 PHE 0.013 0.001 PHE A 129 TYR 0.018 0.001 TYR A 130 ARG 0.008 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.06710 ( 2573) hydrogen bonds : angle 3.53354 ( 7701) covalent geometry : bond 0.00270 (33520) covalent geometry : angle 0.47860 (45284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 452 time to evaluate : 4.297 Fit side-chains REVERT: A 34 TYR cc_start: 0.8098 (m-10) cc_final: 0.7480 (m-10) REVERT: A 141 LYS cc_start: 0.8097 (tttt) cc_final: 0.7698 (tmmt) REVERT: B 107 ASN cc_start: 0.8982 (t0) cc_final: 0.8660 (m-40) REVERT: B 148 ASP cc_start: 0.8517 (m-30) cc_final: 0.7944 (m-30) REVERT: C 78 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: C 111 ASP cc_start: 0.7839 (t0) cc_final: 0.7571 (t0) REVERT: D 68 TYR cc_start: 0.8678 (m-10) cc_final: 0.8425 (m-10) REVERT: D 144 THR cc_start: 0.7834 (t) cc_final: 0.7515 (p) REVERT: E 167 LYS cc_start: 0.7835 (tttm) cc_final: 0.7588 (ttmt) REVERT: F 67 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7835 (tm-30) REVERT: F 125 ASP cc_start: 0.8425 (t0) cc_final: 0.7854 (t0) REVERT: F 137 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8204 (ttp80) REVERT: G 59 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7349 (mt-10) REVERT: G 67 GLU cc_start: 0.7614 (tp30) cc_final: 0.7304 (mm-30) REVERT: G 148 ASP cc_start: 0.8254 (t0) cc_final: 0.7997 (m-30) REVERT: G 157 ASN cc_start: 0.7596 (p0) cc_final: 0.7389 (m-40) REVERT: I 22 GLN cc_start: 0.7574 (mm110) cc_final: 0.7137 (mt0) REVERT: I 81 LYS cc_start: 0.7847 (mttt) cc_final: 0.7520 (mmtp) REVERT: K 56 HIS cc_start: 0.7252 (m-70) cc_final: 0.6882 (t70) REVERT: L 141 LYS cc_start: 0.7184 (tttt) cc_final: 0.6840 (ttpt) REVERT: N 125 ASP cc_start: 0.8610 (t70) cc_final: 0.8386 (t0) REVERT: O 22 GLN cc_start: 0.8065 (tp40) cc_final: 0.7840 (mm-40) REVERT: O 105 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7294 (mmp80) REVERT: Q 22 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7888 (tt0) REVERT: Q 59 GLU cc_start: 0.7818 (tp30) cc_final: 0.7603 (tm-30) REVERT: Q 148 ASP cc_start: 0.8303 (t0) cc_final: 0.8016 (t0) REVERT: R 137 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8105 (ttm170) REVERT: S 56 HIS cc_start: 0.7678 (m-70) cc_final: 0.7324 (t-90) REVERT: S 148 ASP cc_start: 0.7805 (m-30) cc_final: 0.7350 (m-30) REVERT: S 163 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8233 (mm-30) REVERT: T 22 GLN cc_start: 0.8210 (tt0) cc_final: 0.8009 (tt0) REVERT: T 26 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7512 (tp) REVERT: T 34 TYR cc_start: 0.8836 (m-10) cc_final: 0.8541 (m-10) REVERT: T 78 MET cc_start: 0.8290 (mtt) cc_final: 0.7978 (mtt) REVERT: V 67 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7503 (tm-30) REVERT: V 116 ILE cc_start: 0.8313 (mt) cc_final: 0.7928 (mm) REVERT: W 164 GLU cc_start: 0.7056 (tt0) cc_final: 0.6188 (mt-10) REVERT: X 56 HIS cc_start: 0.7129 (t-90) cc_final: 0.6517 (t-90) outliers start: 34 outliers final: 15 residues processed: 470 average time/residue: 1.5755 time to fit residues: 892.2947 Evaluate side-chains 374 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 357 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 274 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS G 27 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN L 23 HIS L 39 HIS Q 56 HIS Q 76 ASN S 27 ASN T 112 HIS W 22 GLN W 154 ASN X 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094267 restraints weight = 317271.880| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 5.15 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33520 Z= 0.235 Angle : 0.555 6.432 45284 Z= 0.314 Chirality : 0.042 0.180 4909 Planarity : 0.004 0.044 5825 Dihedral : 3.886 15.586 4334 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.75 % Allowed : 11.75 % Favored : 85.50 % 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: 1.38 (0.13), residues: 3995 helix: 1.68 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -2.04 (0.16), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 PHE 0.013 0.002 PHE A 129 TYR 0.025 0.002 TYR H 126 ARG 0.008 0.001 ARG M 137 Details of bonding type rmsd hydrogen bonds : bond 0.08895 ( 2573) hydrogen bonds : angle 3.84747 ( 7701) covalent geometry : bond 0.00543 (33520) covalent geometry : angle 0.55471 (45284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 3.691 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: A 141 LYS cc_start: 0.8239 (tttt) cc_final: 0.7761 (ttpt) REVERT: B 107 ASN cc_start: 0.9049 (t0) cc_final: 0.8753 (m-40) REVERT: C 78 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8372 (mtt) REVERT: C 111 ASP cc_start: 0.8054 (t0) cc_final: 0.7768 (t0) REVERT: D 144 THR cc_start: 0.7918 (t) cc_final: 0.7571 (p) REVERT: E 167 LYS cc_start: 0.8042 (tttm) cc_final: 0.7789 (ttmt) REVERT: E 172 LYS cc_start: 0.7693 (tptt) cc_final: 0.6526 (tppt) REVERT: F 67 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7954 (tm-30) REVERT: F 125 ASP cc_start: 0.8343 (t0) cc_final: 0.7823 (t70) REVERT: G 59 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7441 (mt-10) REVERT: G 67 GLU cc_start: 0.7645 (tp30) cc_final: 0.7388 (mm-30) REVERT: G 100 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: G 148 ASP cc_start: 0.8300 (t0) cc_final: 0.8044 (m-30) REVERT: I 22 GLN cc_start: 0.7642 (mm110) cc_final: 0.7268 (mt0) REVERT: I 81 LYS cc_start: 0.8026 (mttt) cc_final: 0.7767 (mmtp) REVERT: K 56 HIS cc_start: 0.7499 (m-70) cc_final: 0.7019 (t70) REVERT: L 79 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7165 (mptt) REVERT: L 125 ASP cc_start: 0.8647 (t70) cc_final: 0.8020 (t70) REVERT: M 59 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: M 101 GLU cc_start: 0.7409 (tp30) cc_final: 0.7113 (mm-30) REVERT: M 164 GLU cc_start: 0.6917 (tt0) cc_final: 0.6647 (tp30) REVERT: N 47 MET cc_start: 0.8769 (mmt) cc_final: 0.8532 (mmt) REVERT: N 125 ASP cc_start: 0.8717 (t0) cc_final: 0.8430 (t0) REVERT: O 22 GLN cc_start: 0.8256 (tp40) cc_final: 0.8034 (mm-40) REVERT: O 55 GLN cc_start: 0.8131 (tp40) cc_final: 0.7725 (tp40) REVERT: O 105 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7387 (mmp80) REVERT: Q 22 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7919 (tt0) REVERT: Q 148 ASP cc_start: 0.8336 (t0) cc_final: 0.8001 (t0) REVERT: Q 169 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7752 (ttm) REVERT: R 137 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8188 (ttm170) REVERT: S 15 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (mmtt) REVERT: S 56 HIS cc_start: 0.7797 (m-70) cc_final: 0.7397 (t-90) REVERT: S 71 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8157 (t70) REVERT: S 148 ASP cc_start: 0.7953 (m-30) cc_final: 0.7518 (m-30) REVERT: T 22 GLN cc_start: 0.8401 (tt0) cc_final: 0.8181 (tt0) REVERT: T 34 TYR cc_start: 0.8926 (m-10) cc_final: 0.8711 (m-10) REVERT: T 78 MET cc_start: 0.8576 (mtt) cc_final: 0.8278 (mtt) REVERT: V 14 ASN cc_start: 0.6791 (t0) cc_final: 0.5800 (t0) REVERT: V 67 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7606 (tm-30) REVERT: V 100 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: W 164 GLU cc_start: 0.6969 (tt0) cc_final: 0.6191 (mt-10) REVERT: X 56 HIS cc_start: 0.7283 (t-90) cc_final: 0.6708 (t-90) outliers start: 67 outliers final: 32 residues processed: 406 average time/residue: 1.2960 time to fit residues: 635.4281 Evaluate side-chains 376 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 169 MET Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 284 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 216 optimal weight: 0.8980 chunk 313 optimal weight: 0.0870 chunk 259 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 ASN K 76 ASN M 154 ASN Q 56 HIS Q 154 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 GLN W 154 ASN X 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105591 restraints weight = 318648.098| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.19 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33520 Z= 0.120 Angle : 0.438 6.343 45284 Z= 0.249 Chirality : 0.037 0.171 4909 Planarity : 0.003 0.038 5825 Dihedral : 3.638 15.487 4334 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.77 % Allowed : 13.32 % Favored : 84.91 % 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: 3995 helix: 2.40 (0.09), residues: 3109 sheet: None (None), residues: 0 loop : -1.37 (0.17), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 PHE 0.012 0.001 PHE Q 53 TYR 0.018 0.001 TYR N 72 ARG 0.008 0.001 ARG M 137 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 2573) hydrogen bonds : angle 3.20165 ( 7701) covalent geometry : bond 0.00217 (33520) covalent geometry : angle 0.43809 (45284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 431 time to evaluate : 4.446 Fit side-chains REVERT: A 141 LYS cc_start: 0.8095 (tttt) cc_final: 0.7759 (tmmt) REVERT: B 107 ASN cc_start: 0.8996 (t0) cc_final: 0.8728 (m-40) REVERT: D 68 TYR cc_start: 0.8750 (m-10) cc_final: 0.8432 (m-10) REVERT: D 138 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7217 (t70) REVERT: F 67 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7923 (tm-30) REVERT: F 105 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7771 (mtt180) REVERT: F 125 ASP cc_start: 0.8337 (t0) cc_final: 0.7742 (t0) REVERT: G 59 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7405 (mt-10) REVERT: I 81 LYS cc_start: 0.7968 (mttt) cc_final: 0.7679 (mmtp) REVERT: I 110 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8014 (mmm-85) REVERT: J 47 MET cc_start: 0.7583 (mmt) cc_final: 0.7269 (mmm) REVERT: J 106 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8522 (mm-30) REVERT: J 150 VAL cc_start: 0.7575 (t) cc_final: 0.7306 (t) REVERT: K 56 HIS cc_start: 0.7445 (m-70) cc_final: 0.6955 (t70) REVERT: K 169 MET cc_start: 0.8980 (ttp) cc_final: 0.8755 (ttm) REVERT: L 79 LYS cc_start: 0.8238 (mptt) cc_final: 0.7661 (ptpt) REVERT: L 141 LYS cc_start: 0.7193 (tttt) cc_final: 0.6985 (ttpt) REVERT: M 56 HIS cc_start: 0.7515 (t-90) cc_final: 0.7223 (t70) REVERT: N 125 ASP cc_start: 0.8411 (t0) cc_final: 0.8157 (t0) REVERT: Q 148 ASP cc_start: 0.8279 (t0) cc_final: 0.8014 (t0) REVERT: R 81 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8394 (mtpm) REVERT: R 89 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8404 (mmtm) REVERT: R 137 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8138 (ttm170) REVERT: S 15 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (mmtt) REVERT: S 47 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6553 (mmt) REVERT: S 56 HIS cc_start: 0.7598 (m-70) cc_final: 0.7257 (t70) REVERT: S 148 ASP cc_start: 0.7673 (m-30) cc_final: 0.7221 (m-30) REVERT: T 78 MET cc_start: 0.8439 (mtt) cc_final: 0.8100 (mtt) REVERT: V 67 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7488 (tm-30) REVERT: V 116 ILE cc_start: 0.8194 (mt) cc_final: 0.7903 (mm) REVERT: W 29 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7870 (mt-10) REVERT: W 164 GLU cc_start: 0.7027 (tt0) cc_final: 0.6304 (mt-10) REVERT: X 56 HIS cc_start: 0.7167 (t-90) cc_final: 0.6648 (t-90) outliers start: 31 outliers final: 13 residues processed: 448 average time/residue: 1.5152 time to fit residues: 837.2282 Evaluate side-chains 365 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 348 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 21 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 301 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN I 157 ASN M 76 ASN N 154 ASN Q 22 GLN Q 56 HIS R 17 ASN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 HIS V 100 GLN W 22 GLN W 154 ASN X 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099567 restraints weight = 323120.362| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 5.17 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33520 Z= 0.156 Angle : 0.476 7.691 45284 Z= 0.269 Chirality : 0.039 0.170 4909 Planarity : 0.003 0.042 5825 Dihedral : 3.606 15.155 4332 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.33 % Allowed : 14.56 % Favored : 83.11 % 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: 2.45 (0.13), residues: 3995 helix: 2.41 (0.09), residues: 3143 sheet: None (None), residues: 0 loop : -1.54 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 PHE 0.013 0.001 PHE Q 53 TYR 0.017 0.001 TYR N 72 ARG 0.011 0.001 ARG K 137 Details of bonding type rmsd hydrogen bonds : bond 0.06833 ( 2573) hydrogen bonds : angle 3.37215 ( 7701) covalent geometry : bond 0.00333 (33520) covalent geometry : angle 0.47628 (45284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 4.170 Fit side-chains REVERT: A 141 LYS cc_start: 0.8160 (tttt) cc_final: 0.7771 (tmmt) REVERT: B 47 MET cc_start: 0.8677 (mmm) cc_final: 0.8104 (mmt) REVERT: B 107 ASN cc_start: 0.9008 (t0) cc_final: 0.8761 (m-40) REVERT: B 125 ASP cc_start: 0.8462 (t0) cc_final: 0.7826 (t70) REVERT: B 158 ASP cc_start: 0.8493 (t0) cc_final: 0.8241 (t0) REVERT: D 68 TYR cc_start: 0.8835 (m-10) cc_final: 0.8489 (m-10) REVERT: D 138 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7259 (t70) REVERT: E 47 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6877 (mmm) REVERT: F 67 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7885 (tm-30) REVERT: F 101 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5586 (tm-30) REVERT: F 125 ASP cc_start: 0.8256 (t0) cc_final: 0.7678 (t0) REVERT: G 59 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7556 (mt-10) REVERT: I 22 GLN cc_start: 0.7575 (mm110) cc_final: 0.7177 (mt0) REVERT: I 81 LYS cc_start: 0.7971 (mttt) cc_final: 0.7673 (mmtp) REVERT: I 110 ARG cc_start: 0.8332 (mtp180) cc_final: 0.8095 (mmm-85) REVERT: I 164 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6194 (tt0) REVERT: K 22 GLN cc_start: 0.8005 (mp10) cc_final: 0.7797 (OUTLIER) REVERT: K 56 HIS cc_start: 0.7573 (m-70) cc_final: 0.7061 (t70) REVERT: L 141 LYS cc_start: 0.7294 (tttt) cc_final: 0.7038 (ttpt) REVERT: M 56 HIS cc_start: 0.7451 (t-90) cc_final: 0.7159 (t-90) REVERT: M 59 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: M 123 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7406 (tm-30) REVERT: M 164 GLU cc_start: 0.6886 (tt0) cc_final: 0.6628 (tp30) REVERT: N 125 ASP cc_start: 0.8530 (t0) cc_final: 0.8162 (t0) REVERT: O 105 ARG cc_start: 0.8122 (mmt90) cc_final: 0.7384 (mmp80) REVERT: Q 148 ASP cc_start: 0.8304 (t0) cc_final: 0.8021 (t0) REVERT: R 89 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8430 (mmtm) REVERT: R 137 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8138 (ttm170) REVERT: S 47 MET cc_start: 0.7777 (mtt) cc_final: 0.7094 (mmt) REVERT: S 56 HIS cc_start: 0.7759 (m-70) cc_final: 0.7358 (t70) REVERT: S 148 ASP cc_start: 0.7803 (m-30) cc_final: 0.7364 (m-30) REVERT: V 67 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7553 (tm-30) REVERT: V 116 ILE cc_start: 0.8361 (mt) cc_final: 0.7999 (mm) REVERT: W 29 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7884 (mt-10) REVERT: W 164 GLU cc_start: 0.7166 (tt0) cc_final: 0.6334 (mt-10) REVERT: X 56 HIS cc_start: 0.7176 (t-90) cc_final: 0.6639 (t-90) outliers start: 51 outliers final: 30 residues processed: 396 average time/residue: 1.3277 time to fit residues: 637.8639 Evaluate side-chains 378 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 157 ASN Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 381 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN Q 56 HIS ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 HIS V 14 ASN V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095405 restraints weight = 333419.258| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.27 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33520 Z= 0.204 Angle : 0.524 7.063 45284 Z= 0.296 Chirality : 0.041 0.179 4909 Planarity : 0.003 0.043 5825 Dihedral : 3.739 15.557 4332 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % 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: 3995 helix: 2.26 (0.09), residues: 3145 sheet: None (None), residues: 0 loop : -1.60 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 PHE 0.013 0.001 PHE Q 53 TYR 0.018 0.002 TYR N 72 ARG 0.010 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.08221 ( 2573) hydrogen bonds : angle 3.63994 ( 7701) covalent geometry : bond 0.00464 (33520) covalent geometry : angle 0.52442 (45284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 5.075 Fit side-chains REVERT: A 141 LYS cc_start: 0.8224 (tttt) cc_final: 0.7822 (tmmt) REVERT: B 107 ASN cc_start: 0.9047 (t0) cc_final: 0.8774 (m-40) REVERT: B 158 ASP cc_start: 0.8505 (t0) cc_final: 0.8230 (t0) REVERT: D 138 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: E 172 LYS cc_start: 0.7639 (tptt) cc_final: 0.6558 (tppt) REVERT: F 67 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7916 (tm-30) REVERT: F 125 ASP cc_start: 0.8336 (t0) cc_final: 0.7770 (t70) REVERT: G 59 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7472 (mt-10) REVERT: H 47 MET cc_start: 0.8506 (mmt) cc_final: 0.8112 (mmt) REVERT: I 22 GLN cc_start: 0.7640 (mm110) cc_final: 0.7263 (mt0) REVERT: I 81 LYS cc_start: 0.7969 (mttt) cc_final: 0.7692 (mmtp) REVERT: I 164 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6065 (tt0) REVERT: K 56 HIS cc_start: 0.7550 (m-70) cc_final: 0.7001 (t70) REVERT: L 79 LYS cc_start: 0.8334 (mptt) cc_final: 0.7695 (ptpt) REVERT: L 141 LYS cc_start: 0.7413 (tttt) cc_final: 0.7066 (ttpt) REVERT: M 59 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: M 101 GLU cc_start: 0.7373 (tp30) cc_final: 0.7101 (mm-30) REVERT: M 123 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7534 (tm-30) REVERT: M 164 GLU cc_start: 0.6920 (tt0) cc_final: 0.6642 (tp30) REVERT: N 125 ASP cc_start: 0.8649 (t0) cc_final: 0.8306 (t0) REVERT: O 22 GLN cc_start: 0.8196 (tp40) cc_final: 0.7962 (mm-40) REVERT: O 105 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7416 (mmp80) REVERT: Q 148 ASP cc_start: 0.8243 (t0) cc_final: 0.7974 (t0) REVERT: R 89 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8401 (mmtm) REVERT: R 137 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8170 (ttm170) REVERT: S 47 MET cc_start: 0.8112 (mtt) cc_final: 0.7461 (mmt) REVERT: S 56 HIS cc_start: 0.7818 (m-70) cc_final: 0.7387 (t70) REVERT: S 148 ASP cc_start: 0.7913 (m-30) cc_final: 0.7476 (m-30) REVERT: V 67 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7543 (tm-30) REVERT: W 75 ARG cc_start: 0.8451 (mtt90) cc_final: 0.8227 (mtt90) REVERT: W 164 GLU cc_start: 0.6996 (tt0) cc_final: 0.6172 (mt-10) REVERT: X 56 HIS cc_start: 0.7158 (t-90) cc_final: 0.6584 (t-90) outliers start: 61 outliers final: 36 residues processed: 386 average time/residue: 1.6848 time to fit residues: 788.1755 Evaluate side-chains 366 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 327 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 315 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 356 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN K 76 ASN N 154 ASN Q 56 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101380 restraints weight = 338064.849| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.32 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33520 Z= 0.132 Angle : 0.454 6.933 45284 Z= 0.257 Chirality : 0.038 0.165 4909 Planarity : 0.003 0.039 5825 Dihedral : 3.611 14.518 4332 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.80 % Allowed : 15.85 % Favored : 82.36 % 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: 2.79 (0.13), residues: 3995 helix: 2.62 (0.09), residues: 3121 sheet: None (None), residues: 0 loop : -1.16 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 PHE 0.013 0.001 PHE Q 53 TYR 0.019 0.001 TYR R 103 ARG 0.009 0.001 ARG K 137 Details of bonding type rmsd hydrogen bonds : bond 0.06183 ( 2573) hydrogen bonds : angle 3.26847 ( 7701) covalent geometry : bond 0.00257 (33520) covalent geometry : angle 0.45377 (45284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 360 time to evaluate : 3.700 Fit side-chains REVERT: A 141 LYS cc_start: 0.8147 (tttt) cc_final: 0.7765 (tmmt) REVERT: B 107 ASN cc_start: 0.8999 (t0) cc_final: 0.8727 (m-40) REVERT: B 125 ASP cc_start: 0.8481 (t0) cc_final: 0.7742 (t70) REVERT: C 34 TYR cc_start: 0.8527 (m-10) cc_final: 0.8254 (m-10) REVERT: C 55 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7885 (tp40) REVERT: D 68 TYR cc_start: 0.8818 (m-10) cc_final: 0.8479 (m-10) REVERT: D 138 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7184 (t70) REVERT: F 67 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 125 ASP cc_start: 0.8259 (t0) cc_final: 0.7673 (t0) REVERT: G 59 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7441 (mt-10) REVERT: I 22 GLN cc_start: 0.7560 (mm110) cc_final: 0.7178 (mt0) REVERT: I 81 LYS cc_start: 0.7970 (mttt) cc_final: 0.7675 (mmtp) REVERT: I 110 ARG cc_start: 0.8282 (mtp180) cc_final: 0.8044 (mmm-85) REVERT: J 47 MET cc_start: 0.7706 (mmt) cc_final: 0.7464 (mmt) REVERT: K 56 HIS cc_start: 0.7485 (m-70) cc_final: 0.6991 (t70) REVERT: L 46 ASP cc_start: 0.8528 (m-30) cc_final: 0.8263 (m-30) REVERT: L 79 LYS cc_start: 0.8272 (mptt) cc_final: 0.7642 (ptpt) REVERT: L 141 LYS cc_start: 0.7229 (tttt) cc_final: 0.6980 (ttpt) REVERT: M 56 HIS cc_start: 0.7488 (t-90) cc_final: 0.7178 (t-90) REVERT: M 123 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7309 (tm-30) REVERT: M 164 GLU cc_start: 0.6912 (tt0) cc_final: 0.6659 (tp30) REVERT: N 125 ASP cc_start: 0.8518 (t0) cc_final: 0.8174 (t0) REVERT: O 105 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7271 (mmp80) REVERT: Q 148 ASP cc_start: 0.8284 (t0) cc_final: 0.7990 (t0) REVERT: R 89 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8426 (mmtm) REVERT: R 137 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8154 (ttm170) REVERT: S 15 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7611 (mmtt) REVERT: S 47 MET cc_start: 0.7686 (mtt) cc_final: 0.7066 (mmt) REVERT: S 56 HIS cc_start: 0.7717 (m-70) cc_final: 0.7337 (t70) REVERT: S 148 ASP cc_start: 0.7770 (m-30) cc_final: 0.7319 (m-30) REVERT: V 67 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7516 (tm-30) REVERT: V 116 ILE cc_start: 0.8292 (mt) cc_final: 0.7962 (mm) REVERT: W 29 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7894 (mt-10) REVERT: W 164 GLU cc_start: 0.7113 (tt0) cc_final: 0.6302 (mt-10) REVERT: X 56 HIS cc_start: 0.7013 (t-90) cc_final: 0.6495 (t-90) outliers start: 31 outliers final: 23 residues processed: 381 average time/residue: 1.3441 time to fit residues: 619.9363 Evaluate side-chains 363 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 338 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 323 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 318 optimal weight: 20.0000 chunk 365 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN E 76 ASN Q 22 GLN Q 56 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 GLN W 154 ASN X 76 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 = 0.116583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100115 restraints weight = 320168.502| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.17 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 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 = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33520 Z= 0.145 Angle : 0.468 7.009 45284 Z= 0.265 Chirality : 0.038 0.174 4909 Planarity : 0.003 0.039 5825 Dihedral : 3.598 14.822 4332 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.02 % 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: 2.83 (0.13), residues: 3995 helix: 2.63 (0.09), residues: 3124 sheet: None (None), residues: 0 loop : -1.10 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 PHE 0.016 0.001 PHE Q 53 TYR 0.023 0.001 TYR H 68 ARG 0.010 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.06599 ( 2573) hydrogen bonds : angle 3.31552 ( 7701) covalent geometry : bond 0.00300 (33520) covalent geometry : angle 0.46787 (45284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 3.399 Fit side-chains REVERT: A 75 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7603 (mtt-85) REVERT: A 141 LYS cc_start: 0.8168 (tttt) cc_final: 0.7784 (tmmt) REVERT: B 107 ASN cc_start: 0.9000 (t0) cc_final: 0.8743 (m-40) REVERT: B 125 ASP cc_start: 0.8446 (t0) cc_final: 0.7722 (t70) REVERT: C 55 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7901 (tp40) REVERT: D 68 TYR cc_start: 0.8834 (m-10) cc_final: 0.8490 (m-10) REVERT: D 138 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7200 (t70) REVERT: E 76 ASN cc_start: 0.8397 (t0) cc_final: 0.8180 (t0) REVERT: F 67 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7878 (tm-30) REVERT: F 125 ASP cc_start: 0.8273 (t0) cc_final: 0.7662 (t0) REVERT: G 59 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7519 (mt-10) REVERT: H 68 TYR cc_start: 0.8607 (m-80) cc_final: 0.8339 (m-80) REVERT: I 22 GLN cc_start: 0.7574 (mm110) cc_final: 0.7192 (mt0) REVERT: I 81 LYS cc_start: 0.7968 (mttt) cc_final: 0.7676 (mmtp) REVERT: I 110 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8082 (mmm-85) REVERT: J 47 MET cc_start: 0.7761 (mmt) cc_final: 0.7483 (mmt) REVERT: K 56 HIS cc_start: 0.7498 (m-70) cc_final: 0.6989 (t70) REVERT: L 46 ASP cc_start: 0.8520 (m-30) cc_final: 0.8244 (m-30) REVERT: L 79 LYS cc_start: 0.8280 (mptt) cc_final: 0.7629 (ptpt) REVERT: L 141 LYS cc_start: 0.7260 (tttt) cc_final: 0.7008 (ttpt) REVERT: M 56 HIS cc_start: 0.7493 (t-90) cc_final: 0.7188 (t-90) REVERT: M 123 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7317 (tm-30) REVERT: M 164 GLU cc_start: 0.6896 (tt0) cc_final: 0.6642 (tp30) REVERT: N 125 ASP cc_start: 0.8534 (t0) cc_final: 0.8166 (t0) REVERT: O 105 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7378 (mmp80) REVERT: Q 148 ASP cc_start: 0.8250 (t0) cc_final: 0.7908 (t0) REVERT: Q 169 MET cc_start: 0.7905 (ttm) cc_final: 0.7380 (ttm) REVERT: R 89 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8421 (mmtm) REVERT: R 137 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8138 (ttm170) REVERT: S 15 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7585 (mmtt) REVERT: S 47 MET cc_start: 0.7796 (mtt) cc_final: 0.7073 (mmt) REVERT: S 56 HIS cc_start: 0.7752 (m-70) cc_final: 0.7352 (t70) REVERT: S 148 ASP cc_start: 0.7816 (m-30) cc_final: 0.7368 (m-30) REVERT: V 67 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7532 (tm-30) REVERT: V 116 ILE cc_start: 0.8330 (mt) cc_final: 0.7978 (mm) REVERT: W 29 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7901 (mt-10) REVERT: W 164 GLU cc_start: 0.7114 (tt0) cc_final: 0.6307 (mt-10) REVERT: X 56 HIS cc_start: 0.7019 (t-90) cc_final: 0.6499 (t-90) outliers start: 43 outliers final: 33 residues processed: 375 average time/residue: 1.2595 time to fit residues: 571.4133 Evaluate side-chains 373 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 338 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 169 MET Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 240 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 ASN Q 22 GLN Q 56 HIS ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093786 restraints weight = 327588.515| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.20 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 33520 Z= 0.242 Angle : 0.559 7.379 45284 Z= 0.315 Chirality : 0.042 0.182 4909 Planarity : 0.003 0.045 5825 Dihedral : 3.807 15.746 4332 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.38 % Allowed : 15.76 % Favored : 81.85 % 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: 2.26 (0.13), residues: 3995 helix: 2.24 (0.09), residues: 3146 sheet: None (None), residues: 0 loop : -1.45 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 PHE 0.015 0.002 PHE Q 53 TYR 0.023 0.002 TYR H 68 ARG 0.010 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.08915 ( 2573) hydrogen bonds : angle 3.76541 ( 7701) covalent geometry : bond 0.00565 (33520) covalent geometry : angle 0.55938 (45284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 3.988 Fit side-chains REVERT: A 75 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7688 (mtt-85) REVERT: A 141 LYS cc_start: 0.8259 (tttt) cc_final: 0.7749 (ttpt) REVERT: B 107 ASN cc_start: 0.9047 (t0) cc_final: 0.8776 (m-40) REVERT: D 138 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: E 172 LYS cc_start: 0.7534 (tptt) cc_final: 0.6675 (tppt) REVERT: F 67 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7927 (tm-30) REVERT: F 101 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6033 (tm-30) REVERT: F 125 ASP cc_start: 0.8403 (t0) cc_final: 0.7793 (t70) REVERT: G 59 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7424 (mt-10) REVERT: G 100 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: G 105 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7031 (mmp80) REVERT: H 47 MET cc_start: 0.8504 (mmt) cc_final: 0.8080 (mmt) REVERT: I 22 GLN cc_start: 0.7661 (mm110) cc_final: 0.7283 (mt0) REVERT: I 81 LYS cc_start: 0.7999 (mttt) cc_final: 0.7707 (mmtp) REVERT: I 164 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6089 (tt0) REVERT: K 56 HIS cc_start: 0.7505 (m-70) cc_final: 0.7003 (t70) REVERT: L 46 ASP cc_start: 0.8559 (m-30) cc_final: 0.8264 (m-30) REVERT: L 67 GLU cc_start: 0.7615 (tt0) cc_final: 0.7277 (tm-30) REVERT: L 79 LYS cc_start: 0.8356 (mptt) cc_final: 0.7700 (ptpt) REVERT: M 59 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: M 101 GLU cc_start: 0.7434 (tp30) cc_final: 0.7167 (mm-30) REVERT: M 123 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7543 (tm-30) REVERT: M 164 GLU cc_start: 0.6933 (tt0) cc_final: 0.6643 (tp30) REVERT: N 71 ASP cc_start: 0.8572 (t0) cc_final: 0.8182 (t0) REVERT: N 125 ASP cc_start: 0.8819 (t0) cc_final: 0.8489 (t0) REVERT: O 22 GLN cc_start: 0.8288 (tp40) cc_final: 0.8061 (mm-40) REVERT: O 55 GLN cc_start: 0.8128 (tp40) cc_final: 0.7717 (tp40) REVERT: O 105 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7408 (mmp80) REVERT: Q 148 ASP cc_start: 0.8237 (t0) cc_final: 0.7954 (t0) REVERT: R 89 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8496 (mmtm) REVERT: R 137 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8186 (ttm170) REVERT: S 15 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7705 (mmtt) REVERT: S 47 MET cc_start: 0.8241 (mtt) cc_final: 0.7449 (mmt) REVERT: S 56 HIS cc_start: 0.7942 (m-70) cc_final: 0.7454 (t70) REVERT: S 148 ASP cc_start: 0.7994 (m-30) cc_final: 0.7576 (m-30) REVERT: V 67 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7605 (tm-30) REVERT: W 164 GLU cc_start: 0.7059 (tt0) cc_final: 0.6208 (mt-10) REVERT: X 56 HIS cc_start: 0.7171 (t-90) cc_final: 0.6603 (t-90) outliers start: 52 outliers final: 34 residues processed: 361 average time/residue: 1.4464 time to fit residues: 638.2986 Evaluate side-chains 356 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 169 MET Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 202 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 363 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 382 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN K 76 ASN Q 22 GLN Q 56 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN W 22 GLN W 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101806 restraints weight = 347888.197| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 5.35 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33520 Z= 0.132 Angle : 0.464 7.857 45284 Z= 0.264 Chirality : 0.038 0.166 4909 Planarity : 0.003 0.040 5825 Dihedral : 3.654 15.623 4332 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.88 % Allowed : 16.44 % Favored : 81.68 % 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: 2.93 (0.13), residues: 3995 helix: 2.69 (0.09), residues: 3121 sheet: None (None), residues: 0 loop : -1.01 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 134 HIS 0.010 0.001 HIS Q 56 PHE 0.014 0.001 PHE Q 53 TYR 0.021 0.001 TYR R 103 ARG 0.009 0.001 ARG M 137 Details of bonding type rmsd hydrogen bonds : bond 0.06023 ( 2573) hydrogen bonds : angle 3.27102 ( 7701) covalent geometry : bond 0.00253 (33520) covalent geometry : angle 0.46443 (45284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7990 Ramachandran restraints generated. 3995 Oldfield, 0 Emsley, 3995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 3.755 Fit side-chains REVERT: A 75 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7589 (mtt-85) REVERT: A 141 LYS cc_start: 0.8218 (tttt) cc_final: 0.7893 (tmmt) REVERT: B 107 ASN cc_start: 0.9039 (t0) cc_final: 0.8768 (m-40) REVERT: B 125 ASP cc_start: 0.8462 (t0) cc_final: 0.7703 (t70) REVERT: C 34 TYR cc_start: 0.8548 (m-10) cc_final: 0.8280 (m-10) REVERT: C 55 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7900 (tp40) REVERT: D 68 TYR cc_start: 0.8881 (m-10) cc_final: 0.8542 (m-10) REVERT: D 78 MET cc_start: 0.8467 (mtt) cc_final: 0.7156 (mtt) REVERT: F 67 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7922 (tm-30) REVERT: F 125 ASP cc_start: 0.8308 (t0) cc_final: 0.7739 (t0) REVERT: G 59 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7495 (mt-10) REVERT: H 68 TYR cc_start: 0.8670 (m-80) cc_final: 0.8374 (m-80) REVERT: I 22 GLN cc_start: 0.7592 (mm110) cc_final: 0.7242 (mt0) REVERT: I 81 LYS cc_start: 0.7979 (mttt) cc_final: 0.7752 (mmtp) REVERT: I 110 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8031 (mmm-85) REVERT: J 47 MET cc_start: 0.7715 (mmt) cc_final: 0.7489 (mmt) REVERT: J 150 VAL cc_start: 0.7821 (t) cc_final: 0.7539 (t) REVERT: K 56 HIS cc_start: 0.7520 (m-70) cc_final: 0.7077 (t70) REVERT: L 46 ASP cc_start: 0.8515 (m-30) cc_final: 0.8241 (m-30) REVERT: L 67 GLU cc_start: 0.7534 (tt0) cc_final: 0.7241 (tm-30) REVERT: L 79 LYS cc_start: 0.8307 (mptt) cc_final: 0.7661 (ptpt) REVERT: L 125 ASP cc_start: 0.8472 (t70) cc_final: 0.7913 (t70) REVERT: L 141 LYS cc_start: 0.7328 (tttt) cc_final: 0.7089 (ttpt) REVERT: M 56 HIS cc_start: 0.7512 (t-90) cc_final: 0.7225 (t70) REVERT: M 123 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7344 (tm-30) REVERT: M 164 GLU cc_start: 0.6935 (tt0) cc_final: 0.6648 (tp30) REVERT: N 125 ASP cc_start: 0.8497 (t0) cc_final: 0.8221 (t0) REVERT: O 105 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7295 (mmp80) REVERT: Q 148 ASP cc_start: 0.8194 (t0) cc_final: 0.7879 (t0) REVERT: Q 169 MET cc_start: 0.7787 (ttm) cc_final: 0.7286 (ttm) REVERT: R 89 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8474 (mmtm) REVERT: S 15 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7543 (mmtt) REVERT: S 47 MET cc_start: 0.7776 (mtt) cc_final: 0.7154 (mmt) REVERT: S 56 HIS cc_start: 0.7725 (m-70) cc_final: 0.7369 (t70) REVERT: S 148 ASP cc_start: 0.7814 (m-30) cc_final: 0.7357 (m-30) REVERT: T 125 ASP cc_start: 0.8406 (t70) cc_final: 0.8122 (t70) REVERT: V 47 MET cc_start: 0.8383 (mmm) cc_final: 0.8147 (mtt) REVERT: V 67 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7543 (tm-30) REVERT: V 116 ILE cc_start: 0.8342 (mt) cc_final: 0.8034 (mm) REVERT: W 164 GLU cc_start: 0.7107 (tt0) cc_final: 0.6287 (mt-10) REVERT: X 56 HIS cc_start: 0.7041 (t-90) cc_final: 0.6559 (t-90) outliers start: 34 outliers final: 23 residues processed: 368 average time/residue: 1.2642 time to fit residues: 566.7505 Evaluate side-chains 359 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 67 GLU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain X residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 37 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 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 55 GLN F 76 ASN M 76 ASN Q 22 GLN Q 56 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 GLN W 154 ASN X 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096713 restraints weight = 338984.708| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.30 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 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 = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33520 Z= 0.187 Angle : 0.509 8.245 45284 Z= 0.287 Chirality : 0.040 0.177 4909 Planarity : 0.003 0.041 5825 Dihedral : 3.697 14.919 4332 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.99 % Allowed : 16.66 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.60 (0.13), residues: 3995 helix: 2.48 (0.09), residues: 3146 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 134 HIS 0.009 0.001 HIS Q 56 PHE 0.017 0.001 PHE Q 53 TYR 0.022 0.002 TYR R 103 ARG 0.011 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.07665 ( 2573) hydrogen bonds : angle 3.51975 ( 7701) covalent geometry : bond 0.00421 (33520) covalent geometry : angle 0.50943 (45284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17619.17 seconds wall clock time: 312 minutes 27.97 seconds (18747.97 seconds total)