Starting phenix.real_space_refine on Tue Aug 26 00:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqv_37755/08_2025/8wqv_37755.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.165 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 20928 2.51 5 N 5321 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32737 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 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: 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: "F" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "G" 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: "H" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "I" 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: "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: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 bond proxies already assigned to first conformer: 1340 Chain: "P" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "Q" 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: "R" 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: "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: 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: "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: 1405 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} bond proxies already assigned to first conformer: 1395 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 13.21, per 1000 atoms: 0.40 Number of scatterers: 32737 At special positions: 0 Unit cell: (130.859, 130.859, 130.859, 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 6392 8.00 N 5321 7.00 C 20928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 2.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7682 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 12 sheets defined 85.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.555A pdb=" N PHE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 123 removed outlier: 3.635A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.750A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'B' and resid 14 through 45 removed outlier: 3.553A 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: 4.622A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 123 removed outlier: 3.573A pdb=" N LEU B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 156' Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'C' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.597A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 123 removed outlier: 3.574A pdb=" N LEU C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.557A 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: 4.597A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 123 removed outlier: 3.588A pdb=" N LEU D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 156 removed outlier: 3.738A pdb=" N SER D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 156' Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'E' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.595A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.585A pdb=" N LEU E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 151 through 156' Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 removed outlier: 3.556A 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: 4.596A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 removed outlier: 3.741A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.656A 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 Processing helix chain 'G' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 123 removed outlier: 3.579A pdb=" N LEU G 98 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 158 through 171 Processing helix chain 'H' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.567A pdb=" N LEU H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 151 through 156' Processing helix chain 'H' and resid 158 through 171 Processing helix chain 'I' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.614A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.571A pdb=" N LEU I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 3.732A pdb=" N SER I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 151 through 156' Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'J' and resid 14 through 45 removed outlier: 3.555A 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: 4.622A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.572A pdb=" N LEU J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 156' Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.600A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.585A pdb=" N LEU K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 156 removed outlier: 3.751A pdb=" N SER K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 151 through 156' Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'L' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU L 98 " --> pdb=" O ASP L 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 removed outlier: 3.753A pdb=" N SER L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 151 through 156' Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'M' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 123 removed outlier: 3.590A pdb=" N LEU M 98 " --> pdb=" O ASP M 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP M 134 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 151 through 156' Processing helix chain 'M' and resid 158 through 171 Processing helix chain 'N' and resid 14 through 45 removed outlier: 3.555A 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: 4.596A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.583A pdb=" N LEU N 98 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 156 removed outlier: 3.740A pdb=" N SER N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 151 through 156' Processing helix chain 'N' and resid 158 through 171 Processing helix chain 'O' and resid 14 through 45 removed outlier: 3.568A pdb=" N PHE O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 55 Processing helix chain 'O' and resid 58 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.625A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.590A pdb=" N LEU O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 156 removed outlier: 3.729A pdb=" N SER O 155 " --> pdb=" O LYS O 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 151 through 156' Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.601A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.569A pdb=" N LEU P 98 " --> pdb=" O ASP P 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER P 155 " --> pdb=" O LYS P 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER P 156 " --> pdb=" O LEU P 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 151 through 156' Processing helix chain 'P' and resid 158 through 171 Processing helix chain 'Q' and resid 14 through 45 removed outlier: 3.556A 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: 4.596A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU Q 98 " --> pdb=" O ASP Q 94 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 156 removed outlier: 3.737A pdb=" N SER Q 155 " --> pdb=" O LYS Q 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER Q 156 " --> pdb=" O LEU Q 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 151 through 156' Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 removed outlier: 3.554A 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: 4.596A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.588A pdb=" N LEU R 98 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER R 155 " --> pdb=" O LYS R 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER R 156 " --> pdb=" O LEU R 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 151 through 156' Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'S' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.571A pdb=" N LEU S 98 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 151 through 156' Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.575A pdb=" N LEU T 98 " --> pdb=" O ASP T 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER T 155 " --> pdb=" O LYS T 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER T 156 " --> pdb=" O LEU T 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 151 through 156' Processing helix chain 'T' and resid 158 through 171 Processing helix chain 'U' and resid 14 through 45 removed outlier: 3.554A 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: 4.601A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.584A pdb=" N LEU U 98 " --> pdb=" O ASP U 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER U 155 " --> pdb=" O LYS U 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER U 156 " --> pdb=" O LEU U 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 151 through 156' Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.621A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU V 98 " --> pdb=" O ASP V 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER V 155 " --> pdb=" O LYS V 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 151 through 156' Processing helix chain 'V' and resid 158 through 171 Processing helix chain 'W' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 123 removed outlier: 3.582A pdb=" N LEU W 98 " --> pdb=" O ASP W 94 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER W 155 " --> pdb=" O LYS W 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER W 156 " --> pdb=" O LEU W 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 151 through 156' Processing helix chain 'W' and resid 158 through 171 Processing helix chain 'X' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.566A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 156 removed outlier: 3.731A pdb=" N SER X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 151 through 156' Processing helix chain 'X' and resid 158 through 172 removed outlier: 3.657A pdb=" N LYS X 172 " --> pdb=" O GLU X 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 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 83 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 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 2588 hydrogen bonds defined for protein. 7785 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: 6.31 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10741 1.34 - 1.46: 4465 1.46 - 1.57: 18054 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33404 Sorted by residual: bond pdb=" CB VAL M 86 " pdb=" CG1 VAL M 86 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" C LEU M 32 " pdb=" O LEU M 32 " ideal model delta sigma weight residual 1.237 1.248 -0.012 1.17e-02 7.31e+03 9.99e-01 bond pdb=" C ALA M 104 " pdb=" O ALA M 104 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.17e-02 7.31e+03 9.14e-01 bond pdb=" C ARG R 137 " pdb=" O ARG R 137 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.96e-01 bond pdb=" C ARG K 137 " pdb=" O ARG K 137 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.96e-01 ... (remaining 33399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 39646 0.81 - 1.62: 4347 1.62 - 2.43: 844 2.43 - 3.23: 236 3.23 - 4.04: 62 Bond angle restraints: 45135 Sorted by residual: angle pdb=" C ARG V 75 " pdb=" N ASN V 76 " pdb=" CA ASN V 76 " ideal model delta sigma weight residual 122.54 119.24 3.30 1.65e+00 3.67e-01 4.01e+00 angle pdb=" C ARG A 75 " pdb=" N ASN A 76 " pdb=" CA ASN A 76 " ideal model delta sigma weight residual 122.54 119.25 3.29 1.65e+00 3.67e-01 3.98e+00 angle pdb=" C ARG X 75 " pdb=" N ASN X 76 " pdb=" CA ASN X 76 " ideal model delta sigma weight residual 122.54 119.26 3.28 1.65e+00 3.67e-01 3.96e+00 angle pdb=" CA TYR P 126 " pdb=" CB TYR P 126 " pdb=" CG TYR P 126 " ideal model delta sigma weight residual 113.90 110.32 3.58 1.80e+00 3.09e-01 3.96e+00 angle pdb=" C ARG B 75 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 122.54 119.26 3.28 1.65e+00 3.67e-01 3.95e+00 ... (remaining 45130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 17684 17.06 - 34.12: 1913 34.12 - 51.19: 326 51.19 - 68.25: 73 68.25 - 85.31: 55 Dihedral angle restraints: 20051 sinusoidal: 8144 harmonic: 11907 Sorted by residual: dihedral pdb=" CA ASP A 94 " pdb=" C ASP A 94 " pdb=" N ALA A 95 " pdb=" CA ALA A 95 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP M 94 " pdb=" C ASP M 94 " pdb=" N ALA M 95 " pdb=" CA ALA M 95 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP H 94 " pdb=" C ASP H 94 " pdb=" N ALA H 95 " pdb=" CA ALA H 95 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 20048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2211 0.025 - 0.050: 1506 0.050 - 0.075: 856 0.075 - 0.100: 140 0.100 - 0.125: 184 Chirality restraints: 4897 Sorted by residual: chirality pdb=" CA ILE I 91 " pdb=" N ILE I 91 " pdb=" C ILE I 91 " pdb=" CB ILE I 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE S 91 " pdb=" N ILE S 91 " pdb=" C ILE S 91 " pdb=" CB ILE S 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ASN S 76 " pdb=" N ASN S 76 " pdb=" C ASN S 76 " pdb=" CB ASN S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 4894 not shown) Planarity restraints: 5807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 126 " 0.016 2.00e-02 2.50e+03 9.29e-03 1.73e+00 pdb=" CG TYR U 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR U 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR U 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR U 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR U 126 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR U 126 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 126 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 126 " 0.016 2.00e-02 2.50e+03 9.28e-03 1.72e+00 pdb=" CG TYR T 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR T 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR T 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR T 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR T 126 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR T 126 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 126 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 126 " 0.016 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR V 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR V 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR V 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR V 126 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR V 126 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 126 " 0.004 2.00e-02 2.50e+03 ... (remaining 5804 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.13: 23515 3.13 - 3.72: 49299 3.72 - 4.31: 71494 4.31 - 4.90: 118851 Nonbonded interactions: 263254 Sorted by model distance: nonbonded pdb=" OD2 ASP E 138 " pdb="FE FE E 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP W 138 " pdb="FE FE W 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP C 138 " pdb="FE FE C 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP L 138 " pdb="FE FE L 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP R 138 " pdb="FE FE R 201 " model vdw 1.957 2.260 ... (remaining 263249 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 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 37.630 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.090 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 33404 Z= 0.268 Angle : 0.591 4.044 45135 Z= 0.345 Chirality : 0.043 0.125 4897 Planarity : 0.004 0.032 5807 Dihedral : 14.833 85.311 12369 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.35 % Allowed : 2.67 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.11), residues: 3985 helix: -0.50 (0.08), residues: 3141 sheet: None (None), residues: 0 loop : -2.78 (0.12), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 105 TYR 0.020 0.003 TYR U 126 PHE 0.009 0.002 PHE N 153 TRP 0.009 0.002 TRP X 180 HIS 0.004 0.001 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00608 (33404) covalent geometry : angle 0.59122 (45135) hydrogen bonds : bond 0.15725 ( 2588) hydrogen bonds : angle 4.80456 ( 7785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.313 Fit side-chains REVERT: A 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7650 (mtmt) REVERT: B 55 GLN cc_start: 0.8354 (tp40) cc_final: 0.8148 (tp-100) REVERT: B 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7667 (mtmt) REVERT: C 151 LYS cc_start: 0.8364 (pttm) cc_final: 0.7648 (mtmt) REVERT: D 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7659 (mtmt) REVERT: E 151 LYS cc_start: 0.8366 (pttm) cc_final: 0.7648 (mtmt) REVERT: F 151 LYS cc_start: 0.8369 (pttm) cc_final: 0.7652 (mtmt) REVERT: G 151 LYS cc_start: 0.8361 (pttm) cc_final: 0.7642 (mtmt) REVERT: H 55 GLN cc_start: 0.8360 (tp40) cc_final: 0.8150 (tp-100) REVERT: H 151 LYS cc_start: 0.8375 (pttm) cc_final: 0.7660 (mtmt) REVERT: I 151 LYS cc_start: 0.8385 (pttm) cc_final: 0.7671 (mtmt) REVERT: J 151 LYS cc_start: 0.8372 (pttm) cc_final: 0.7662 (mtmt) REVERT: K 141 LYS cc_start: 0.7885 (tttt) cc_final: 0.7678 (ttpt) REVERT: K 151 LYS cc_start: 0.8366 (pttm) cc_final: 0.7648 (mtmt) REVERT: L 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7652 (mtmt) REVERT: M 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7655 (mtmt) REVERT: N 151 LYS cc_start: 0.8382 (pttm) cc_final: 0.7668 (mtmt) REVERT: O 141 LYS cc_start: 0.7885 (tttt) cc_final: 0.7681 (ttpt) REVERT: O 151 LYS cc_start: 0.8363 (pttm) cc_final: 0.7645 (mtmt) REVERT: P 151 LYS cc_start: 0.8377 (pttm) cc_final: 0.7668 (mtmt) REVERT: Q 151 LYS cc_start: 0.8367 (pttm) cc_final: 0.7645 (mtmt) REVERT: R 151 LYS cc_start: 0.8377 (pttm) cc_final: 0.7660 (mtmt) REVERT: S 151 LYS cc_start: 0.8372 (pttm) cc_final: 0.7659 (mtmt) REVERT: T 55 GLN cc_start: 0.8357 (tp40) cc_final: 0.8149 (tp-100) REVERT: T 151 LYS cc_start: 0.8364 (pttm) cc_final: 0.7648 (mtmt) REVERT: U 141 LYS cc_start: 0.7897 (tttt) cc_final: 0.7694 (ttpt) REVERT: U 151 LYS cc_start: 0.8369 (pttm) cc_final: 0.7655 (mtmt) REVERT: V 55 GLN cc_start: 0.8361 (tp40) cc_final: 0.8148 (tp-100) REVERT: V 151 LYS cc_start: 0.8368 (pttm) cc_final: 0.7656 (mtmt) REVERT: W 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7665 (mtmt) REVERT: X 114 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7910 (tttt) REVERT: X 141 LYS cc_start: 0.7931 (tttt) cc_final: 0.7691 (ttpt) REVERT: X 151 LYS cc_start: 0.8378 (pttm) cc_final: 0.7664 (mtmt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.9665 time to fit residues: 573.0593 Evaluate side-chains 358 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 39 HIS A 55 GLN A 76 ASN B 14 ASN B 39 HIS B 76 ASN C 14 ASN C 39 HIS C 55 GLN C 76 ASN D 14 ASN D 39 HIS D 55 GLN D 76 ASN E 14 ASN E 39 HIS E 55 GLN E 76 ASN F 14 ASN F 39 HIS F 55 GLN F 76 ASN G 14 ASN G 39 HIS G 55 GLN G 76 ASN H 14 ASN H 39 HIS H 76 ASN I 14 ASN I 39 HIS I 55 GLN I 76 ASN J 14 ASN J 39 HIS J 76 ASN K 14 ASN K 39 HIS K 55 GLN K 76 ASN L 14 ASN L 39 HIS L 55 GLN L 76 ASN M 14 ASN M 39 HIS M 55 GLN M 76 ASN N 14 ASN N 39 HIS N 55 GLN N 76 ASN O 14 ASN O 39 HIS O 76 ASN P 14 ASN P 39 HIS P 55 GLN P 76 ASN Q 14 ASN Q 39 HIS Q 55 GLN Q 76 ASN R 14 ASN R 39 HIS R 55 GLN R 76 ASN S 14 ASN S 39 HIS S 55 GLN S 76 ASN T 14 ASN T 39 HIS T 76 ASN U 14 ASN U 39 HIS U 55 GLN U 76 ASN V 14 ASN V 39 HIS V 76 ASN W 14 ASN W 39 HIS W 55 GLN W 76 ASN X 14 ASN X 39 HIS X 55 GLN X 76 ASN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125581 restraints weight = 210004.612| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.05 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 33404 Z= 0.137 Angle : 0.425 3.509 45135 Z= 0.247 Chirality : 0.036 0.116 4897 Planarity : 0.003 0.030 5807 Dihedral : 4.035 14.091 4321 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.28 % Allowed : 8.89 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 3985 helix: 1.39 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 110 TYR 0.008 0.001 TYR X 49 PHE 0.004 0.001 PHE J 53 TRP 0.005 0.001 TRP J 180 HIS 0.002 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00232 (33404) covalent geometry : angle 0.42476 (45135) hydrogen bonds : bond 0.07160 ( 2588) hydrogen bonds : angle 3.57026 ( 7785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 443 time to evaluate : 1.383 Fit side-chains REVERT: A 76 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8080 (p0) REVERT: A 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7393 (t70) REVERT: B 55 GLN cc_start: 0.8493 (tp40) cc_final: 0.8271 (tp-100) REVERT: B 76 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7373 (t70) REVERT: C 76 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8077 (p0) REVERT: C 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7385 (t70) REVERT: D 76 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8079 (p0) REVERT: D 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7418 (t70) REVERT: E 76 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8035 (p0) REVERT: E 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7387 (t70) REVERT: F 76 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (p0) REVERT: F 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7414 (t70) REVERT: G 76 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8044 (p0) REVERT: G 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7391 (t70) REVERT: H 55 GLN cc_start: 0.8491 (tp40) cc_final: 0.8271 (tp-100) REVERT: H 76 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7973 (p0) REVERT: H 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7382 (t70) REVERT: I 76 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8039 (p0) REVERT: I 111 ASP cc_start: 0.7658 (t0) cc_final: 0.7379 (t70) REVERT: J 76 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7984 (p0) REVERT: J 111 ASP cc_start: 0.7665 (t0) cc_final: 0.7386 (t70) REVERT: K 76 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8068 (p0) REVERT: K 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7400 (t70) REVERT: L 76 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8086 (p0) REVERT: L 111 ASP cc_start: 0.7674 (t0) cc_final: 0.7415 (t70) REVERT: M 76 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8007 (p0) REVERT: M 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7377 (t70) REVERT: N 76 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (p0) REVERT: N 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7380 (t70) REVERT: O 76 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.8026 (p0) REVERT: O 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7393 (t70) REVERT: O 151 LYS cc_start: 0.8271 (pttm) cc_final: 0.7670 (mtmt) REVERT: P 76 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8066 (p0) REVERT: P 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7354 (t70) REVERT: Q 76 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8024 (p0) REVERT: Q 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7399 (t70) REVERT: R 76 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8082 (p0) REVERT: R 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7404 (t70) REVERT: S 76 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8054 (p0) REVERT: S 111 ASP cc_start: 0.7696 (t0) cc_final: 0.7419 (t70) REVERT: T 55 GLN cc_start: 0.8502 (tp40) cc_final: 0.8277 (tp-100) REVERT: T 76 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (p0) REVERT: T 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7365 (t70) REVERT: U 76 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8058 (p0) REVERT: U 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7375 (t70) REVERT: V 55 GLN cc_start: 0.8512 (tp40) cc_final: 0.8280 (tp-100) REVERT: V 76 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7980 (p0) REVERT: V 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7392 (t70) REVERT: W 76 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8048 (p0) REVERT: W 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7377 (t70) REVERT: X 76 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8033 (p0) REVERT: X 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7425 (t70) outliers start: 33 outliers final: 9 residues processed: 443 average time/residue: 0.7555 time to fit residues: 394.2930 Evaluate side-chains 391 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 140 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 chunk 377 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 329 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121756 restraints weight = 229126.204| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.30 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 33404 Z= 0.146 Angle : 0.425 3.215 45135 Z= 0.247 Chirality : 0.037 0.116 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.870 13.668 4321 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.59 % Allowed : 11.43 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.12), residues: 3985 helix: 1.95 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.62 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 110 TYR 0.013 0.001 TYR V 126 PHE 0.005 0.001 PHE J 53 TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00269 (33404) covalent geometry : angle 0.42523 (45135) hydrogen bonds : bond 0.07722 ( 2588) hydrogen bonds : angle 3.57303 ( 7785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 387 time to evaluate : 1.355 Fit side-chains REVERT: A 76 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7411 (t70) REVERT: A 151 LYS cc_start: 0.8216 (pttm) cc_final: 0.7641 (mtmt) REVERT: B 55 GLN cc_start: 0.8495 (tp40) cc_final: 0.8271 (tp-100) REVERT: B 76 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7388 (t70) REVERT: B 151 LYS cc_start: 0.8301 (pttm) cc_final: 0.7726 (mtmt) REVERT: C 76 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7990 (p0) REVERT: C 111 ASP cc_start: 0.7692 (t0) cc_final: 0.7431 (t70) REVERT: D 76 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7991 (p0) REVERT: D 111 ASP cc_start: 0.7712 (t0) cc_final: 0.7434 (t70) REVERT: D 151 LYS cc_start: 0.8225 (pttm) cc_final: 0.7649 (mtmt) REVERT: E 76 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.8012 (p0) REVERT: E 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7367 (t70) REVERT: E 151 LYS cc_start: 0.8235 (pttm) cc_final: 0.7654 (mtmt) REVERT: F 76 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (p0) REVERT: F 111 ASP cc_start: 0.7715 (t0) cc_final: 0.7465 (t70) REVERT: F 151 LYS cc_start: 0.8217 (pttm) cc_final: 0.7633 (mtmt) REVERT: G 76 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7992 (p0) REVERT: G 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7414 (t70) REVERT: H 55 GLN cc_start: 0.8491 (tp40) cc_final: 0.8270 (tp-100) REVERT: H 76 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7974 (p0) REVERT: H 111 ASP cc_start: 0.7694 (t0) cc_final: 0.7407 (t70) REVERT: H 151 LYS cc_start: 0.8316 (pttm) cc_final: 0.7755 (mtmt) REVERT: I 76 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.8009 (p0) REVERT: I 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7389 (t70) REVERT: I 151 LYS cc_start: 0.8266 (pttm) cc_final: 0.7661 (mtmt) REVERT: J 76 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7970 (p0) REVERT: J 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7402 (t70) REVERT: J 151 LYS cc_start: 0.8217 (pttm) cc_final: 0.7643 (mtmt) REVERT: K 76 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7977 (p0) REVERT: K 111 ASP cc_start: 0.7690 (t0) cc_final: 0.7416 (t70) REVERT: K 151 LYS cc_start: 0.8238 (pttm) cc_final: 0.7669 (mtmt) REVERT: L 76 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7999 (p0) REVERT: L 111 ASP cc_start: 0.7708 (t0) cc_final: 0.7458 (t70) REVERT: L 151 LYS cc_start: 0.8306 (pttm) cc_final: 0.7726 (mtmt) REVERT: M 76 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7985 (p0) REVERT: M 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7409 (t70) REVERT: M 151 LYS cc_start: 0.8210 (pttm) cc_final: 0.7624 (mtmt) REVERT: N 76 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8024 (p0) REVERT: N 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7350 (t70) REVERT: N 151 LYS cc_start: 0.8228 (pttm) cc_final: 0.7651 (mtmt) REVERT: O 76 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8021 (p0) REVERT: O 111 ASP cc_start: 0.7698 (t0) cc_final: 0.7442 (t70) REVERT: O 151 LYS cc_start: 0.8284 (pttm) cc_final: 0.7690 (mtmt) REVERT: P 76 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.8002 (p0) REVERT: P 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7418 (t70) REVERT: P 151 LYS cc_start: 0.8229 (pttm) cc_final: 0.7663 (mtmt) REVERT: Q 76 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7989 (p0) REVERT: Q 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7395 (t70) REVERT: Q 151 LYS cc_start: 0.8202 (pttm) cc_final: 0.7617 (mtmt) REVERT: R 76 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7988 (p0) REVERT: R 111 ASP cc_start: 0.7738 (t0) cc_final: 0.7461 (t70) REVERT: R 151 LYS cc_start: 0.8237 (pttm) cc_final: 0.7669 (mtmt) REVERT: S 76 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (p0) REVERT: S 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7405 (t70) REVERT: S 151 LYS cc_start: 0.8267 (pttm) cc_final: 0.7682 (mtmt) REVERT: T 55 GLN cc_start: 0.8505 (tp40) cc_final: 0.8277 (tp-100) REVERT: T 76 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7946 (p0) REVERT: T 111 ASP cc_start: 0.7656 (t0) cc_final: 0.7363 (t70) REVERT: T 151 LYS cc_start: 0.8226 (pttm) cc_final: 0.7646 (mtmt) REVERT: U 76 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7992 (p0) REVERT: U 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7402 (t70) REVERT: V 55 GLN cc_start: 0.8511 (tp40) cc_final: 0.8279 (tp-100) REVERT: V 76 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7992 (p0) REVERT: V 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7417 (t70) REVERT: V 151 LYS cc_start: 0.8321 (pttm) cc_final: 0.7748 (mtmt) REVERT: W 76 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.8007 (p0) REVERT: W 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7345 (t70) REVERT: W 151 LYS cc_start: 0.8306 (pttm) cc_final: 0.7733 (mtmt) REVERT: X 76 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7997 (p0) REVERT: X 111 ASP cc_start: 0.7727 (t0) cc_final: 0.7445 (t70) outliers start: 63 outliers final: 9 residues processed: 387 average time/residue: 0.8113 time to fit residues: 363.7348 Evaluate side-chains 371 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 338 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 326 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 348 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122439 restraints weight = 220787.567| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.14 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 33404 Z= 0.145 Angle : 0.418 3.402 45135 Z= 0.243 Chirality : 0.037 0.114 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.800 13.120 4321 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.60 % Allowed : 12.47 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.12), residues: 3985 helix: 2.23 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.56 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 110 TYR 0.013 0.001 TYR A 126 PHE 0.005 0.001 PHE Q 153 TRP 0.004 0.001 TRP S 180 HIS 0.002 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00264 (33404) covalent geometry : angle 0.41841 (45135) hydrogen bonds : bond 0.07659 ( 2588) hydrogen bonds : angle 3.57838 ( 7785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 354 time to evaluate : 1.265 Fit side-chains REVERT: A 76 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p0) REVERT: A 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7422 (t70) REVERT: A 151 LYS cc_start: 0.8247 (pttm) cc_final: 0.7671 (mtmt) REVERT: B 55 GLN cc_start: 0.8495 (tp40) cc_final: 0.8275 (tp-100) REVERT: B 76 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7865 (p0) REVERT: B 111 ASP cc_start: 0.7680 (t0) cc_final: 0.7428 (t70) REVERT: B 151 LYS cc_start: 0.8238 (pttm) cc_final: 0.7651 (mtmt) REVERT: C 76 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7900 (p0) REVERT: C 111 ASP cc_start: 0.7698 (t0) cc_final: 0.7451 (t70) REVERT: C 151 LYS cc_start: 0.8267 (pttm) cc_final: 0.7688 (mtmt) REVERT: D 76 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7905 (p0) REVERT: D 111 ASP cc_start: 0.7710 (t0) cc_final: 0.7471 (t70) REVERT: D 151 LYS cc_start: 0.8248 (pttm) cc_final: 0.7679 (mtmt) REVERT: E 76 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7926 (p0) REVERT: E 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7423 (t70) REVERT: E 151 LYS cc_start: 0.8261 (pttm) cc_final: 0.7686 (mtmt) REVERT: F 76 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7909 (p0) REVERT: F 111 ASP cc_start: 0.7708 (t0) cc_final: 0.7467 (t70) REVERT: F 151 LYS cc_start: 0.8246 (pttm) cc_final: 0.7665 (mtmt) REVERT: G 76 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7911 (p0) REVERT: G 111 ASP cc_start: 0.7700 (t0) cc_final: 0.7449 (t70) REVERT: H 55 GLN cc_start: 0.8499 (tp40) cc_final: 0.8280 (tp-100) REVERT: H 76 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (p0) REVERT: H 111 ASP cc_start: 0.7694 (t0) cc_final: 0.7445 (t70) REVERT: H 151 LYS cc_start: 0.8264 (pttm) cc_final: 0.7697 (mtmt) REVERT: I 76 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7917 (p0) REVERT: I 111 ASP cc_start: 0.7675 (t0) cc_final: 0.7421 (t70) REVERT: I 151 LYS cc_start: 0.8140 (pttm) cc_final: 0.7587 (mtmt) REVERT: J 76 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7850 (p0) REVERT: J 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7420 (t70) REVERT: J 151 LYS cc_start: 0.8256 (pttm) cc_final: 0.7684 (mtmt) REVERT: K 76 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7895 (p0) REVERT: K 111 ASP cc_start: 0.7716 (t0) cc_final: 0.7471 (t70) REVERT: K 151 LYS cc_start: 0.8270 (pttm) cc_final: 0.7706 (mtmt) REVERT: L 76 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7915 (p0) REVERT: L 111 ASP cc_start: 0.7712 (t0) cc_final: 0.7470 (t70) REVERT: L 151 LYS cc_start: 0.8249 (pttm) cc_final: 0.7667 (mtmt) REVERT: M 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7425 (t70) REVERT: M 151 LYS cc_start: 0.8252 (pttm) cc_final: 0.7674 (mtmt) REVERT: N 76 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7937 (p0) REVERT: N 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7410 (t70) REVERT: N 151 LYS cc_start: 0.8265 (pttm) cc_final: 0.7699 (mtmt) REVERT: O 76 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (p0) REVERT: O 111 ASP cc_start: 0.7709 (t0) cc_final: 0.7466 (t70) REVERT: O 151 LYS cc_start: 0.8108 (pttm) cc_final: 0.7549 (mtmm) REVERT: P 76 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7918 (p0) REVERT: P 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7428 (t70) REVERT: P 151 LYS cc_start: 0.8268 (pttm) cc_final: 0.7702 (mtmt) REVERT: Q 76 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7904 (p0) REVERT: Q 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7432 (t70) REVERT: Q 151 LYS cc_start: 0.8243 (pttm) cc_final: 0.7663 (mtmt) REVERT: R 76 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7885 (p0) REVERT: R 111 ASP cc_start: 0.7732 (t0) cc_final: 0.7488 (t70) REVERT: R 151 LYS cc_start: 0.8262 (pttm) cc_final: 0.7698 (mtmt) REVERT: S 76 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7921 (p0) REVERT: S 111 ASP cc_start: 0.7687 (t0) cc_final: 0.7439 (t70) REVERT: S 151 LYS cc_start: 0.8264 (pttm) cc_final: 0.7695 (mtmt) REVERT: T 55 GLN cc_start: 0.8509 (tp40) cc_final: 0.8286 (tp-100) REVERT: T 76 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7864 (p0) REVERT: T 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7403 (t70) REVERT: T 151 LYS cc_start: 0.8267 (pttm) cc_final: 0.7691 (mtmt) REVERT: U 76 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7907 (p0) REVERT: U 111 ASP cc_start: 0.7709 (t0) cc_final: 0.7462 (t70) REVERT: V 55 GLN cc_start: 0.8513 (tp40) cc_final: 0.8285 (tp-100) REVERT: V 76 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7881 (p0) REVERT: V 111 ASP cc_start: 0.7676 (t0) cc_final: 0.7427 (t70) REVERT: V 151 LYS cc_start: 0.8248 (pttm) cc_final: 0.7664 (mtmt) REVERT: W 76 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (p0) REVERT: W 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7391 (t70) REVERT: W 151 LYS cc_start: 0.8243 (pttm) cc_final: 0.7663 (mtmt) REVERT: X 76 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7907 (p0) REVERT: X 111 ASP cc_start: 0.7720 (t0) cc_final: 0.7475 (t70) outliers start: 33 outliers final: 9 residues processed: 354 average time/residue: 0.7882 time to fit residues: 324.2797 Evaluate side-chains 368 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 290 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121295 restraints weight = 224680.209| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.22 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 33404 Z= 0.150 Angle : 0.420 3.310 45135 Z= 0.243 Chirality : 0.037 0.114 4897 Planarity : 0.003 0.032 5807 Dihedral : 3.781 13.086 4321 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.05 % Allowed : 12.02 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.12), residues: 3985 helix: 2.37 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.52 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 110 TYR 0.013 0.001 TYR B 126 PHE 0.006 0.001 PHE V 153 TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00280 (33404) covalent geometry : angle 0.41961 (45135) hydrogen bonds : bond 0.07895 ( 2588) hydrogen bonds : angle 3.57735 ( 7785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 1.324 Fit side-chains REVERT: A 76 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7428 (t70) REVERT: A 151 LYS cc_start: 0.8122 (pttm) cc_final: 0.7564 (mtmt) REVERT: B 55 GLN cc_start: 0.8478 (tp40) cc_final: 0.8260 (tp-100) REVERT: B 76 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 151 LYS cc_start: 0.8097 (pttm) cc_final: 0.7525 (mtmt) REVERT: C 76 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 151 LYS cc_start: 0.8131 (pttm) cc_final: 0.7570 (mtmt) REVERT: D 76 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (p0) REVERT: D 111 ASP cc_start: 0.7745 (t0) cc_final: 0.7513 (t70) REVERT: D 151 LYS cc_start: 0.8127 (pttm) cc_final: 0.7573 (mtmt) REVERT: E 76 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7913 (p0) REVERT: E 151 LYS cc_start: 0.8130 (pttm) cc_final: 0.7569 (mtmt) REVERT: F 76 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7893 (p0) REVERT: F 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7479 (t70) REVERT: F 151 LYS cc_start: 0.8121 (pttm) cc_final: 0.7558 (mtmt) REVERT: H 55 GLN cc_start: 0.8476 (tp40) cc_final: 0.8254 (tp-100) REVERT: H 151 LYS cc_start: 0.8137 (pttm) cc_final: 0.7586 (mtmt) REVERT: I 151 LYS cc_start: 0.8091 (pttm) cc_final: 0.7484 (mtmm) REVERT: J 151 LYS cc_start: 0.8138 (pttm) cc_final: 0.7589 (mtmt) REVERT: K 76 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7882 (p0) REVERT: K 111 ASP cc_start: 0.7750 (t0) cc_final: 0.7512 (t70) REVERT: K 151 LYS cc_start: 0.8139 (pttm) cc_final: 0.7588 (mtmt) REVERT: L 76 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (p0) REVERT: L 111 ASP cc_start: 0.7704 (t0) cc_final: 0.7462 (t70) REVERT: L 151 LYS cc_start: 0.8118 (pttm) cc_final: 0.7553 (mtmt) REVERT: M 151 LYS cc_start: 0.8121 (pttm) cc_final: 0.7560 (mtmt) REVERT: N 76 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (p0) REVERT: N 151 LYS cc_start: 0.8133 (pttm) cc_final: 0.7577 (mtmt) REVERT: O 76 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7909 (p0) REVERT: O 151 LYS cc_start: 0.7977 (pttm) cc_final: 0.7359 (mtmm) REVERT: P 76 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7909 (p0) REVERT: P 151 LYS cc_start: 0.8146 (pttm) cc_final: 0.7599 (mtmt) REVERT: Q 151 LYS cc_start: 0.8110 (pttm) cc_final: 0.7551 (mtmt) REVERT: R 76 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7865 (p0) REVERT: R 111 ASP cc_start: 0.7776 (t0) cc_final: 0.7544 (t70) REVERT: R 151 LYS cc_start: 0.8140 (pttm) cc_final: 0.7593 (mtmt) REVERT: S 151 LYS cc_start: 0.8120 (pttm) cc_final: 0.7567 (mtmt) REVERT: T 55 GLN cc_start: 0.8492 (tp40) cc_final: 0.8270 (tp-100) REVERT: T 151 LYS cc_start: 0.8133 (pttm) cc_final: 0.7574 (mtmt) REVERT: U 76 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (p0) REVERT: U 111 ASP cc_start: 0.7740 (t0) cc_final: 0.7498 (t70) REVERT: V 55 GLN cc_start: 0.8491 (tp40) cc_final: 0.8265 (tp-100) REVERT: V 151 LYS cc_start: 0.8118 (pttm) cc_final: 0.7549 (mtmt) REVERT: W 151 LYS cc_start: 0.8115 (pttm) cc_final: 0.7553 (mtmt) REVERT: X 76 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7915 (p0) REVERT: X 111 ASP cc_start: 0.7750 (t0) cc_final: 0.7512 (t70) outliers start: 49 outliers final: 9 residues processed: 358 average time/residue: 0.7405 time to fit residues: 308.9830 Evaluate side-chains 334 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 168 optimal weight: 0.0870 chunk 381 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 371 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 296 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127195 restraints weight = 216018.325| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.23 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33404 Z= 0.119 Angle : 0.383 3.147 45135 Z= 0.225 Chirality : 0.035 0.112 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.628 12.802 4321 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.75 % Allowed : 12.33 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.12), residues: 3985 helix: 2.68 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.35 (0.16), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.010 0.001 TYR A 126 PHE 0.005 0.001 PHE J 53 TRP 0.003 0.001 TRP X 180 HIS 0.002 0.000 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00195 (33404) covalent geometry : angle 0.38336 (45135) hydrogen bonds : bond 0.06196 ( 2588) hydrogen bonds : angle 3.41860 ( 7785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 1.183 Fit side-chains REVERT: A 111 ASP cc_start: 0.7602 (t0) cc_final: 0.7399 (t70) REVERT: B 111 ASP cc_start: 0.7701 (t0) cc_final: 0.7383 (t70) REVERT: C 111 ASP cc_start: 0.7696 (t0) cc_final: 0.7377 (t70) REVERT: D 111 ASP cc_start: 0.7648 (t0) cc_final: 0.7444 (t70) REVERT: E 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7387 (t70) REVERT: G 111 ASP cc_start: 0.7713 (t0) cc_final: 0.7398 (t70) REVERT: H 111 ASP cc_start: 0.7701 (t0) cc_final: 0.7388 (t70) REVERT: I 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7363 (t70) REVERT: J 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7361 (t70) REVERT: K 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7434 (t70) REVERT: L 111 ASP cc_start: 0.7625 (t0) cc_final: 0.7420 (t70) REVERT: M 111 ASP cc_start: 0.7698 (t0) cc_final: 0.7383 (t70) REVERT: N 76 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7644 (p0) REVERT: N 111 ASP cc_start: 0.7676 (t0) cc_final: 0.7356 (t70) REVERT: O 111 ASP cc_start: 0.7700 (t0) cc_final: 0.7382 (t70) REVERT: P 76 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7640 (p0) REVERT: P 111 ASP cc_start: 0.7654 (t0) cc_final: 0.7334 (t70) REVERT: Q 111 ASP cc_start: 0.7684 (t0) cc_final: 0.7367 (t70) REVERT: R 111 ASP cc_start: 0.7676 (t0) cc_final: 0.7471 (t70) REVERT: S 111 ASP cc_start: 0.7700 (t0) cc_final: 0.7388 (t70) REVERT: T 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7344 (t70) REVERT: U 76 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7603 (p0) REVERT: U 111 ASP cc_start: 0.7633 (t0) cc_final: 0.7426 (t70) REVERT: V 111 ASP cc_start: 0.7646 (t0) cc_final: 0.7321 (t70) REVERT: W 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7337 (t70) REVERT: X 111 ASP cc_start: 0.7645 (t0) cc_final: 0.7436 (t70) outliers start: 38 outliers final: 0 residues processed: 337 average time/residue: 0.7415 time to fit residues: 294.3286 Evaluate side-chains 301 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 125 optimal weight: 9.9990 chunk 348 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 324 optimal weight: 0.9980 chunk 272 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 312 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128357 restraints weight = 211318.676| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.19 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 33404 Z= 0.117 Angle : 0.378 3.101 45135 Z= 0.222 Chirality : 0.035 0.143 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.540 12.209 4321 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.29 % Allowed : 12.89 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.13), residues: 3985 helix: 2.79 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.98 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 75 TYR 0.010 0.001 TYR W 126 PHE 0.005 0.001 PHE J 53 TRP 0.002 0.001 TRP Q 180 HIS 0.002 0.001 HIS J 39 Details of bonding type rmsd covalent geometry : bond 0.00190 (33404) covalent geometry : angle 0.37843 (45135) hydrogen bonds : bond 0.06027 ( 2588) hydrogen bonds : angle 3.36872 ( 7785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 371 time to evaluate : 1.404 Fit side-chains REVERT: A 111 ASP cc_start: 0.7598 (t0) cc_final: 0.7397 (t70) REVERT: B 111 ASP cc_start: 0.7641 (t0) cc_final: 0.7335 (t70) REVERT: C 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7382 (t70) REVERT: E 111 ASP cc_start: 0.7641 (t0) cc_final: 0.7336 (t70) REVERT: G 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7358 (t70) REVERT: H 111 ASP cc_start: 0.7665 (t0) cc_final: 0.7363 (t70) REVERT: I 111 ASP cc_start: 0.7637 (t0) cc_final: 0.7334 (t70) REVERT: J 111 ASP cc_start: 0.7632 (t0) cc_final: 0.7328 (t70) REVERT: K 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7432 (t70) REVERT: L 111 ASP cc_start: 0.7623 (t0) cc_final: 0.7420 (t70) REVERT: M 76 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7839 (p0) REVERT: M 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7342 (t70) REVERT: N 76 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7724 (p0) REVERT: N 111 ASP cc_start: 0.7635 (t0) cc_final: 0.7327 (t70) REVERT: O 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7370 (t70) REVERT: P 76 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7710 (p0) REVERT: P 111 ASP cc_start: 0.7640 (t0) cc_final: 0.7333 (t70) REVERT: Q 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7336 (t70) REVERT: R 111 ASP cc_start: 0.7660 (t0) cc_final: 0.7455 (t70) REVERT: S 111 ASP cc_start: 0.7649 (t0) cc_final: 0.7344 (t70) REVERT: T 111 ASP cc_start: 0.7630 (t0) cc_final: 0.7324 (t70) REVERT: U 76 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (p0) REVERT: U 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7431 (t70) REVERT: V 111 ASP cc_start: 0.7666 (t0) cc_final: 0.7361 (t70) REVERT: W 111 ASP cc_start: 0.7610 (t0) cc_final: 0.7305 (t70) REVERT: X 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7460 (t70) outliers start: 22 outliers final: 0 residues processed: 380 average time/residue: 0.7512 time to fit residues: 335.2108 Evaluate side-chains 329 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 180 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 0.3980 chunk 344 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 76 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN ** V 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126727 restraints weight = 223492.497| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.27 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33404 Z= 0.123 Angle : 0.384 3.386 45135 Z= 0.226 Chirality : 0.036 0.108 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.548 12.244 4321 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.21 % Allowed : 13.62 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.17 (0.13), residues: 3985 helix: 2.77 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.79 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 75 TYR 0.011 0.001 TYR V 24 PHE 0.005 0.001 PHE J 53 TRP 0.003 0.001 TRP V 180 HIS 0.002 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00208 (33404) covalent geometry : angle 0.38382 (45135) hydrogen bonds : bond 0.06403 ( 2588) hydrogen bonds : angle 3.43140 ( 7785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 1.198 Fit side-chains REVERT: A 111 ASP cc_start: 0.7621 (t0) cc_final: 0.7410 (t70) REVERT: B 55 GLN cc_start: 0.8468 (tp40) cc_final: 0.8250 (tp-100) REVERT: B 111 ASP cc_start: 0.7656 (t0) cc_final: 0.7351 (t70) REVERT: C 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7376 (t70) REVERT: E 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7357 (t70) REVERT: G 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7374 (t70) REVERT: H 55 GLN cc_start: 0.8472 (tp40) cc_final: 0.8253 (tp-100) REVERT: H 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7363 (t70) REVERT: I 76 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7963 (p0) REVERT: I 111 ASP cc_start: 0.7641 (t0) cc_final: 0.7337 (t70) REVERT: J 111 ASP cc_start: 0.7649 (t0) cc_final: 0.7342 (t70) REVERT: K 111 ASP cc_start: 0.7658 (t0) cc_final: 0.7456 (t70) REVERT: L 111 ASP cc_start: 0.7652 (t0) cc_final: 0.7447 (t70) REVERT: M 76 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7653 (p0) REVERT: M 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7338 (t70) REVERT: N 76 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7669 (p0) REVERT: N 111 ASP cc_start: 0.7629 (t0) cc_final: 0.7327 (t70) REVERT: O 111 ASP cc_start: 0.7680 (t0) cc_final: 0.7376 (t70) REVERT: P 76 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (p0) REVERT: P 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7338 (t70) REVERT: Q 76 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7945 (p0) REVERT: Q 111 ASP cc_start: 0.7653 (t0) cc_final: 0.7347 (t70) REVERT: R 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7462 (t70) REVERT: S 111 ASP cc_start: 0.7658 (t0) cc_final: 0.7354 (t70) REVERT: T 55 GLN cc_start: 0.8485 (tp40) cc_final: 0.8262 (tp-100) REVERT: T 111 ASP cc_start: 0.7635 (t0) cc_final: 0.7326 (t70) REVERT: U 76 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7623 (p0) REVERT: U 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7451 (t70) REVERT: V 55 GLN cc_start: 0.8480 (tp40) cc_final: 0.8253 (tp-100) REVERT: V 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7361 (t70) REVERT: W 111 ASP cc_start: 0.7613 (t0) cc_final: 0.7304 (t70) REVERT: X 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7467 (t70) outliers start: 19 outliers final: 10 residues processed: 353 average time/residue: 0.6587 time to fit residues: 274.0561 Evaluate side-chains 336 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 360 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 362 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 chunk 284 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124712 restraints weight = 213479.967| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.18 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33404 Z= 0.133 Angle : 0.399 3.516 45135 Z= 0.234 Chirality : 0.036 0.150 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.581 12.365 4321 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.32 % Allowed : 13.82 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.12), residues: 3985 helix: 2.72 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.72 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 75 TYR 0.011 0.001 TYR B 126 PHE 0.005 0.001 PHE G 153 TRP 0.003 0.001 TRP O 180 HIS 0.002 0.001 HIS M 36 Details of bonding type rmsd covalent geometry : bond 0.00236 (33404) covalent geometry : angle 0.39912 (45135) hydrogen bonds : bond 0.06963 ( 2588) hydrogen bonds : angle 3.49050 ( 7785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 327 time to evaluate : 1.307 Fit side-chains REVERT: A 111 ASP cc_start: 0.7623 (t0) cc_final: 0.7409 (t70) REVERT: B 55 GLN cc_start: 0.8458 (tp40) cc_final: 0.8233 (tp-100) REVERT: B 111 ASP cc_start: 0.7656 (t0) cc_final: 0.7349 (t70) REVERT: C 111 ASP cc_start: 0.7672 (t0) cc_final: 0.7369 (t70) REVERT: E 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7335 (t70) REVERT: G 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7372 (t70) REVERT: H 55 GLN cc_start: 0.8463 (tp40) cc_final: 0.8238 (tp-100) REVERT: H 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7361 (t70) REVERT: I 76 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7849 (p0) REVERT: I 111 ASP cc_start: 0.7640 (t0) cc_final: 0.7334 (t70) REVERT: J 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7333 (t70) REVERT: K 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7454 (t70) REVERT: L 111 ASP cc_start: 0.7649 (t0) cc_final: 0.7436 (t70) REVERT: M 76 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (p0) REVERT: M 111 ASP cc_start: 0.7652 (t0) cc_final: 0.7348 (t70) REVERT: N 76 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7982 (p0) REVERT: N 111 ASP cc_start: 0.7622 (t0) cc_final: 0.7314 (t70) REVERT: O 111 ASP cc_start: 0.7676 (t0) cc_final: 0.7378 (t70) REVERT: P 76 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7971 (p0) REVERT: P 111 ASP cc_start: 0.7654 (t0) cc_final: 0.7345 (t70) REVERT: Q 76 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7854 (p0) REVERT: Q 111 ASP cc_start: 0.7646 (t0) cc_final: 0.7340 (t70) REVERT: R 111 ASP cc_start: 0.7670 (t0) cc_final: 0.7452 (t70) REVERT: S 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7349 (t70) REVERT: T 55 GLN cc_start: 0.8479 (tp40) cc_final: 0.8247 (tp-100) REVERT: T 111 ASP cc_start: 0.7635 (t0) cc_final: 0.7327 (t70) REVERT: U 76 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7948 (p0) REVERT: U 111 ASP cc_start: 0.7653 (t0) cc_final: 0.7439 (t70) REVERT: V 55 GLN cc_start: 0.8471 (tp40) cc_final: 0.8240 (tp-100) REVERT: V 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7355 (t70) REVERT: W 111 ASP cc_start: 0.7606 (t0) cc_final: 0.7300 (t70) REVERT: X 111 ASP cc_start: 0.7676 (t0) cc_final: 0.7460 (t70) outliers start: 23 outliers final: 0 residues processed: 343 average time/residue: 0.6668 time to fit residues: 270.1721 Evaluate side-chains 332 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 326 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118891 restraints weight = 230211.361| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.23 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 33404 Z= 0.179 Angle : 0.458 3.738 45135 Z= 0.265 Chirality : 0.039 0.154 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.754 12.774 4321 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.88 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.12), residues: 3985 helix: 2.43 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -0.84 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 75 TYR 0.014 0.002 TYR V 126 PHE 0.010 0.002 PHE Q 73 TRP 0.004 0.001 TRP A 180 HIS 0.003 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00363 (33404) covalent geometry : angle 0.45803 (45135) hydrogen bonds : bond 0.08907 ( 2588) hydrogen bonds : angle 3.72317 ( 7785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 323 time to evaluate : 1.162 Fit side-chains REVERT: A 111 ASP cc_start: 0.7716 (t0) cc_final: 0.7499 (t70) REVERT: A 151 LYS cc_start: 0.8053 (pttm) cc_final: 0.7427 (mtmm) REVERT: B 55 GLN cc_start: 0.8444 (tp40) cc_final: 0.8231 (tp-100) REVERT: B 111 ASP cc_start: 0.7713 (t0) cc_final: 0.7406 (t70) REVERT: B 151 LYS cc_start: 0.8019 (pttm) cc_final: 0.7369 (mtmm) REVERT: C 111 ASP cc_start: 0.7744 (t0) cc_final: 0.7440 (t70) REVERT: C 151 LYS cc_start: 0.8044 (pttm) cc_final: 0.7402 (mtmm) REVERT: D 151 LYS cc_start: 0.8048 (pttm) cc_final: 0.7417 (mtmm) REVERT: E 111 ASP cc_start: 0.7695 (t0) cc_final: 0.7387 (t70) REVERT: E 151 LYS cc_start: 0.8048 (pttm) cc_final: 0.7414 (mtmm) REVERT: F 151 LYS cc_start: 0.8051 (pttm) cc_final: 0.7411 (mtmm) REVERT: G 111 ASP cc_start: 0.7727 (t0) cc_final: 0.7422 (t70) REVERT: G 151 LYS cc_start: 0.8083 (pttm) cc_final: 0.7427 (mtmm) REVERT: H 55 GLN cc_start: 0.8457 (tp40) cc_final: 0.8243 (tp-100) REVERT: H 111 ASP cc_start: 0.7739 (t0) cc_final: 0.7439 (t70) REVERT: H 151 LYS cc_start: 0.8052 (pttm) cc_final: 0.7420 (mtmm) REVERT: I 76 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8134 (p0) REVERT: I 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7399 (t70) REVERT: I 151 LYS cc_start: 0.8055 (pttm) cc_final: 0.7402 (mtmm) REVERT: J 111 ASP cc_start: 0.7714 (t0) cc_final: 0.7414 (t70) REVERT: J 151 LYS cc_start: 0.8050 (pttm) cc_final: 0.7420 (mtmm) REVERT: K 111 ASP cc_start: 0.7739 (t0) cc_final: 0.7524 (t70) REVERT: K 151 LYS cc_start: 0.8065 (pttm) cc_final: 0.7436 (mtmm) REVERT: L 111 ASP cc_start: 0.7746 (t0) cc_final: 0.7527 (t70) REVERT: L 151 LYS cc_start: 0.8039 (pttm) cc_final: 0.7396 (mtmm) REVERT: M 111 ASP cc_start: 0.7711 (t0) cc_final: 0.7405 (t70) REVERT: M 151 LYS cc_start: 0.8019 (pttm) cc_final: 0.7367 (mtmm) REVERT: N 111 ASP cc_start: 0.7687 (t0) cc_final: 0.7382 (t70) REVERT: N 151 LYS cc_start: 0.8058 (pttm) cc_final: 0.7427 (mtmm) REVERT: O 111 ASP cc_start: 0.7743 (t0) cc_final: 0.7444 (t70) REVERT: O 151 LYS cc_start: 0.8012 (pttm) cc_final: 0.7390 (mtmm) REVERT: P 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7419 (t70) REVERT: P 151 LYS cc_start: 0.8059 (pttm) cc_final: 0.7432 (mtmm) REVERT: Q 76 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8130 (p0) REVERT: Q 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7401 (t70) REVERT: Q 151 LYS cc_start: 0.8034 (pttm) cc_final: 0.7394 (mtmm) REVERT: R 111 ASP cc_start: 0.7771 (t0) cc_final: 0.7556 (t70) REVERT: R 151 LYS cc_start: 0.8051 (pttm) cc_final: 0.7423 (mtmm) REVERT: S 111 ASP cc_start: 0.7724 (t0) cc_final: 0.7426 (t70) REVERT: S 151 LYS cc_start: 0.8054 (pttm) cc_final: 0.7419 (mtmm) REVERT: T 55 GLN cc_start: 0.8466 (tp40) cc_final: 0.8249 (tp-100) REVERT: T 111 ASP cc_start: 0.7691 (t0) cc_final: 0.7385 (t70) REVERT: T 151 LYS cc_start: 0.8042 (pttm) cc_final: 0.7401 (mtmm) REVERT: U 111 ASP cc_start: 0.7760 (t0) cc_final: 0.7548 (t70) REVERT: V 55 GLN cc_start: 0.8460 (tp40) cc_final: 0.8239 (tp-100) REVERT: V 111 ASP cc_start: 0.7694 (t0) cc_final: 0.7390 (t70) REVERT: V 151 LYS cc_start: 0.8046 (pttm) cc_final: 0.7409 (mtmm) REVERT: W 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7364 (t70) REVERT: W 151 LYS cc_start: 0.8026 (pttm) cc_final: 0.7388 (mtmm) REVERT: X 111 ASP cc_start: 0.7761 (t0) cc_final: 0.7544 (t70) REVERT: X 151 LYS cc_start: 0.8071 (pttm) cc_final: 0.7435 (mtmm) outliers start: 24 outliers final: 2 residues processed: 332 average time/residue: 0.8189 time to fit residues: 315.0015 Evaluate side-chains 313 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 309 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain V residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 361 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN R 76 ASN S 76 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122077 restraints weight = 221593.904| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.12 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33404 Z= 0.144 Angle : 0.416 4.857 45135 Z= 0.244 Chirality : 0.037 0.114 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.694 12.775 4321 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.21 % Allowed : 13.96 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.12), residues: 3985 helix: 2.59 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.69 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 75 TYR 0.013 0.001 TYR A 126 PHE 0.007 0.001 PHE S 153 TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS M 36 Details of bonding type rmsd covalent geometry : bond 0.00244 (33404) covalent geometry : angle 0.41555 (45135) hydrogen bonds : bond 0.07774 ( 2588) hydrogen bonds : angle 3.62342 ( 7785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7932.15 seconds wall clock time: 136 minutes 41.44 seconds (8201.44 seconds total)