Starting phenix.real_space_refine on Fri Jun 27 16:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqv_37755/06_2025/8wqv_37755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqv_37755/06_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_37755/06_2025/8wqv_37755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqv_37755/06_2025/8wqv_37755.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqv_37755/06_2025/8wqv_37755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqv_37755/06_2025/8wqv_37755.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 33.31, per 1000 atoms: 1.02 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: 8.34 Conformation dependent library (CDL) restraints added in 6.8 seconds 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: 2.53 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: 11.62 Time building geometry restraints manager: 9.99 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 181 or resid 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 181 or resid 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 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 181 or resid 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 181 or resid 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 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 181 or resid 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 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 181 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.040 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 89.730 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (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 TRP 0.009 0.002 TRP X 180 HIS 0.004 0.001 HIS K 36 PHE 0.009 0.002 PHE N 153 TYR 0.020 0.003 TYR U 126 ARG 0.004 0.001 ARG R 105 Details of bonding type rmsd hydrogen bonds : bond 0.15725 ( 2588) hydrogen bonds : angle 4.80456 ( 7785) covalent geometry : bond 0.00608 (33404) covalent geometry : angle 0.59122 (45135) *********************** 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 : 4.084 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: 1.8816 time to fit residues: 1121.0797 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 : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.148605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126146 restraints weight = 210259.716| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.15 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33404 Z= 0.132 Angle : 0.419 3.538 45135 Z= 0.244 Chirality : 0.036 0.116 4897 Planarity : 0.003 0.030 5807 Dihedral : 4.007 13.866 4321 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.28 % Allowed : 8.81 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 3985 helix: 1.41 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 180 HIS 0.002 0.001 HIS A 36 PHE 0.004 0.001 PHE T 53 TYR 0.008 0.001 TYR X 49 ARG 0.001 0.000 ARG F 110 Details of bonding type rmsd hydrogen bonds : bond 0.06930 ( 2588) hydrogen bonds : angle 3.55245 ( 7785) covalent geometry : bond 0.00220 (33404) covalent geometry : angle 0.41909 (45135) *********************** 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 475 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 442 time to evaluate : 3.642 Fit side-chains REVERT: A 76 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (p0) REVERT: A 111 ASP cc_start: 0.7634 (t0) cc_final: 0.7346 (t70) REVERT: B 55 GLN cc_start: 0.8480 (tp40) cc_final: 0.8257 (tp-100) REVERT: B 76 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 111 ASP cc_start: 0.7645 (t0) cc_final: 0.7357 (t70) REVERT: C 76 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8028 (p0) REVERT: C 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7358 (t70) REVERT: D 76 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7401 (t70) REVERT: E 76 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8031 (p0) REVERT: E 111 ASP cc_start: 0.7647 (t0) cc_final: 0.7360 (t70) REVERT: F 76 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.8025 (p0) REVERT: F 111 ASP cc_start: 0.7651 (t0) cc_final: 0.7386 (t70) REVERT: G 76 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8034 (p0) REVERT: G 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7357 (t70) REVERT: H 55 GLN cc_start: 0.8465 (tp40) cc_final: 0.8232 (tp-100) REVERT: H 76 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7982 (p0) REVERT: H 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7356 (t70) REVERT: I 76 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8010 (p0) REVERT: I 111 ASP cc_start: 0.7642 (t0) cc_final: 0.7356 (t70) REVERT: J 76 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (p0) REVERT: J 111 ASP cc_start: 0.7647 (t0) cc_final: 0.7361 (t70) REVERT: K 76 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.8014 (p0) REVERT: K 111 ASP cc_start: 0.7664 (t0) cc_final: 0.7378 (t70) REVERT: L 76 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.8029 (p0) REVERT: L 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7375 (t70) REVERT: M 76 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7989 (p0) REVERT: M 111 ASP cc_start: 0.7641 (t0) cc_final: 0.7359 (t70) REVERT: N 76 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.8047 (p0) REVERT: N 111 ASP cc_start: 0.7654 (t0) cc_final: 0.7369 (t70) REVERT: O 76 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8046 (p0) REVERT: O 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7377 (t70) REVERT: O 151 LYS cc_start: 0.8247 (pttm) cc_final: 0.7636 (mtmt) REVERT: P 76 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.8012 (p0) REVERT: P 111 ASP cc_start: 0.7617 (t0) cc_final: 0.7329 (t70) REVERT: Q 76 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8022 (p0) REVERT: Q 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7379 (t70) REVERT: R 76 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.8030 (p0) REVERT: R 111 ASP cc_start: 0.7647 (t0) cc_final: 0.7365 (t70) REVERT: S 76 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8050 (p0) REVERT: S 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7392 (t70) REVERT: T 55 GLN cc_start: 0.8489 (tp40) cc_final: 0.8266 (tp-100) REVERT: T 76 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7990 (p0) REVERT: T 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7355 (t70) REVERT: U 76 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.8010 (p0) REVERT: U 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7354 (t70) REVERT: V 55 GLN cc_start: 0.8500 (tp40) cc_final: 0.8268 (tp-100) REVERT: V 76 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7981 (p0) REVERT: V 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7379 (t70) REVERT: W 76 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.8042 (p0) REVERT: W 111 ASP cc_start: 0.7644 (t0) cc_final: 0.7358 (t70) REVERT: X 76 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (p0) REVERT: X 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7383 (t70) outliers start: 33 outliers final: 7 residues processed: 442 average time/residue: 1.5019 time to fit residues: 797.9952 Evaluate side-chains 378 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 347 time to evaluate : 3.763 ------------------------------------------------------------------------------- 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 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 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 160 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 350 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 0.0000 chunk 83 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.144379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121503 restraints weight = 226247.924| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.20 r_work (final): 0.3408 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33404 Z= 0.152 Angle : 0.431 3.107 45135 Z= 0.250 Chirality : 0.037 0.116 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.875 13.807 4321 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.86 % Allowed : 12.10 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.12), residues: 3985 helix: 1.90 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.63 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS M 36 PHE 0.005 0.001 PHE J 53 TYR 0.013 0.001 TYR V 126 ARG 0.001 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.07957 ( 2588) hydrogen bonds : angle 3.61100 ( 7785) covalent geometry : bond 0.00285 (33404) covalent geometry : angle 0.43131 (45135) *********************** 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 424 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 390 time to evaluate : 3.679 Fit side-chains REVERT: A 76 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 111 ASP cc_start: 0.7646 (t0) cc_final: 0.7396 (t70) REVERT: A 151 LYS cc_start: 0.8322 (pttm) cc_final: 0.7759 (mtmt) REVERT: B 55 GLN cc_start: 0.8496 (tp40) cc_final: 0.8271 (tp-100) REVERT: B 76 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 111 ASP cc_start: 0.7692 (t0) cc_final: 0.7401 (t70) REVERT: B 151 LYS cc_start: 0.8314 (pttm) cc_final: 0.7745 (mtmt) REVERT: C 76 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8073 (p0) REVERT: C 111 ASP cc_start: 0.7695 (t0) cc_final: 0.7433 (t70) REVERT: C 151 LYS cc_start: 0.8334 (pttm) cc_final: 0.7772 (mtmt) REVERT: D 76 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8076 (p0) REVERT: D 111 ASP cc_start: 0.7715 (t0) cc_final: 0.7438 (t70) REVERT: D 151 LYS cc_start: 0.8325 (pttm) cc_final: 0.7765 (mtmt) REVERT: E 76 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8087 (p0) REVERT: E 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7388 (t70) REVERT: E 151 LYS cc_start: 0.8234 (pttm) cc_final: 0.7655 (mtmt) REVERT: F 76 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8074 (p0) REVERT: F 111 ASP cc_start: 0.7723 (t0) cc_final: 0.7472 (t70) REVERT: F 151 LYS cc_start: 0.8324 (pttm) cc_final: 0.7752 (mtmt) REVERT: G 76 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8077 (p0) REVERT: G 111 ASP cc_start: 0.7701 (t0) cc_final: 0.7413 (t70) REVERT: H 55 GLN cc_start: 0.8498 (tp40) cc_final: 0.8277 (tp-100) REVERT: H 76 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8023 (p0) REVERT: H 111 ASP cc_start: 0.7691 (t0) cc_final: 0.7403 (t70) REVERT: H 151 LYS cc_start: 0.8330 (pttm) cc_final: 0.7775 (mtmt) REVERT: I 76 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8090 (p0) REVERT: I 111 ASP cc_start: 0.7689 (t0) cc_final: 0.7400 (t70) REVERT: I 151 LYS cc_start: 0.8297 (pttm) cc_final: 0.7692 (mtmt) REVERT: J 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7400 (t70) REVERT: J 151 LYS cc_start: 0.8243 (pttm) cc_final: 0.7675 (mtmt) REVERT: K 76 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8071 (p0) REVERT: K 111 ASP cc_start: 0.7704 (t0) cc_final: 0.7431 (t70) REVERT: K 151 LYS cc_start: 0.8335 (pttm) cc_final: 0.7785 (mtmt) REVERT: L 76 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8083 (p0) REVERT: L 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7427 (t70) REVERT: L 151 LYS cc_start: 0.8323 (pttm) cc_final: 0.7745 (mtmt) REVERT: M 76 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8065 (p0) REVERT: M 111 ASP cc_start: 0.7684 (t0) cc_final: 0.7423 (t70) REVERT: M 151 LYS cc_start: 0.8231 (pttm) cc_final: 0.7653 (mtmt) REVERT: N 76 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8098 (p0) REVERT: N 111 ASP cc_start: 0.7660 (t0) cc_final: 0.7366 (t70) REVERT: N 151 LYS cc_start: 0.8325 (pttm) cc_final: 0.7760 (mtmt) REVERT: O 76 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8127 (p0) REVERT: O 111 ASP cc_start: 0.7707 (t0) cc_final: 0.7452 (t70) REVERT: O 151 LYS cc_start: 0.8289 (pttm) cc_final: 0.7693 (mtmt) REVERT: P 76 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (p0) REVERT: P 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7404 (t70) REVERT: P 151 LYS cc_start: 0.8246 (pttm) cc_final: 0.7682 (mtmt) REVERT: Q 76 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8074 (p0) REVERT: Q 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7403 (t70) REVERT: Q 151 LYS cc_start: 0.8320 (pttm) cc_final: 0.7750 (mtmt) REVERT: R 76 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8067 (p0) REVERT: R 111 ASP cc_start: 0.7715 (t0) cc_final: 0.7443 (t70) REVERT: R 151 LYS cc_start: 0.8254 (pttm) cc_final: 0.7690 (mtmt) REVERT: S 76 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8079 (p0) REVERT: S 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7403 (t70) REVERT: S 151 LYS cc_start: 0.8328 (pttm) cc_final: 0.7768 (mtmt) REVERT: T 55 GLN cc_start: 0.8514 (tp40) cc_final: 0.8285 (tp-100) REVERT: T 76 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8031 (p0) REVERT: T 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7373 (t70) REVERT: T 151 LYS cc_start: 0.8247 (pttm) cc_final: 0.7672 (mtmt) REVERT: U 76 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8076 (p0) REVERT: U 111 ASP cc_start: 0.7680 (t0) cc_final: 0.7402 (t70) REVERT: V 55 GLN cc_start: 0.8518 (tp40) cc_final: 0.8280 (tp-100) REVERT: V 76 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.8075 (p0) REVERT: V 111 ASP cc_start: 0.7686 (t0) cc_final: 0.7426 (t70) REVERT: V 151 LYS cc_start: 0.8226 (pttm) cc_final: 0.7647 (mtmt) REVERT: W 76 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (p0) REVERT: W 111 ASP cc_start: 0.7647 (t0) cc_final: 0.7355 (t70) REVERT: W 151 LYS cc_start: 0.8323 (pttm) cc_final: 0.7758 (mtmt) REVERT: X 76 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.8056 (p0) REVERT: X 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7422 (t70) outliers start: 34 outliers final: 9 residues processed: 390 average time/residue: 1.6639 time to fit residues: 752.8530 Evaluate side-chains 369 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 337 time to evaluate : 3.542 ------------------------------------------------------------------------------- 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 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 335 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 308 optimal weight: 0.7980 chunk 284 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 E 76 ASN G 76 ASN H 76 ASN J 76 ASN L 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127610 restraints weight = 223708.223| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.24 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2220 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= 0.119 Angle : 0.386 3.174 45135 Z= 0.226 Chirality : 0.036 0.114 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.669 12.995 4321 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.38 % Allowed : 12.72 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.13), residues: 3985 helix: 2.47 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.53 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 180 HIS 0.002 0.001 HIS H 39 PHE 0.005 0.001 PHE J 53 TYR 0.009 0.001 TYR P 126 ARG 0.001 0.000 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.06175 ( 2588) hydrogen bonds : angle 3.41927 ( 7785) covalent geometry : bond 0.00195 (33404) covalent geometry : angle 0.38569 (45135) *********************** 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 367 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 342 time to evaluate : 4.091 Fit side-chains REVERT: A 76 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 111 ASP cc_start: 0.7652 (t0) cc_final: 0.7421 (t70) REVERT: B 76 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7659 (p0) REVERT: B 111 ASP cc_start: 0.7686 (t0) cc_final: 0.7446 (t70) REVERT: C 111 ASP cc_start: 0.7694 (t0) cc_final: 0.7463 (t70) REVERT: D 111 ASP cc_start: 0.7709 (t0) cc_final: 0.7481 (t70) REVERT: E 76 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (p0) REVERT: E 111 ASP cc_start: 0.7670 (t0) cc_final: 0.7431 (t70) REVERT: F 111 ASP cc_start: 0.7717 (t0) cc_final: 0.7489 (t70) REVERT: G 76 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7666 (p0) REVERT: G 111 ASP cc_start: 0.7687 (t0) cc_final: 0.7447 (t70) REVERT: H 76 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7654 (p0) REVERT: H 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7444 (t70) REVERT: I 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7424 (t70) REVERT: J 111 ASP cc_start: 0.7672 (t0) cc_final: 0.7442 (t70) REVERT: K 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7461 (t70) REVERT: L 76 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7671 (p0) REVERT: L 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7435 (t70) REVERT: M 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7443 (t70) REVERT: N 76 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7691 (p0) REVERT: N 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7424 (t70) REVERT: O 76 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7693 (p0) REVERT: O 111 ASP cc_start: 0.7692 (t0) cc_final: 0.7463 (t70) REVERT: P 76 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7670 (p0) REVERT: P 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7436 (t70) REVERT: Q 76 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7696 (p0) REVERT: Q 111 ASP cc_start: 0.7674 (t0) cc_final: 0.7436 (t70) REVERT: R 76 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7657 (p0) REVERT: R 111 ASP cc_start: 0.7736 (t0) cc_final: 0.7502 (t70) REVERT: S 76 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7645 (p0) REVERT: S 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7442 (t70) REVERT: T 111 ASP cc_start: 0.7658 (t0) cc_final: 0.7419 (t70) REVERT: U 111 ASP cc_start: 0.7702 (t0) cc_final: 0.7463 (t70) REVERT: V 76 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7624 (p0) REVERT: V 111 ASP cc_start: 0.7684 (t0) cc_final: 0.7453 (t70) REVERT: W 76 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7674 (p0) REVERT: W 111 ASP cc_start: 0.7653 (t0) cc_final: 0.7413 (t70) REVERT: X 76 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7696 (p0) REVERT: X 111 ASP cc_start: 0.7721 (t0) cc_final: 0.7485 (t70) outliers start: 25 outliers final: 7 residues processed: 342 average time/residue: 1.5648 time to fit residues: 635.9803 Evaluate side-chains 357 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 335 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B 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 89 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L 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 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 324 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 339 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 299 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125815 restraints weight = 227446.688| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 4.22 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2112 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= 0.130 Angle : 0.394 3.136 45135 Z= 0.229 Chirality : 0.036 0.142 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.634 12.416 4321 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 12.64 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.13), residues: 3985 helix: 2.59 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.48 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 180 HIS 0.002 0.001 HIS D 36 PHE 0.005 0.001 PHE J 53 TYR 0.011 0.001 TYR T 24 ARG 0.001 0.000 ARG Q 75 Details of bonding type rmsd hydrogen bonds : bond 0.06842 ( 2588) hydrogen bonds : angle 3.46520 ( 7785) covalent geometry : bond 0.00227 (33404) covalent geometry : angle 0.39382 (45135) *********************** 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 372 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 342 time to evaluate : 4.776 Fit side-chains REVERT: A 76 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (p0) REVERT: A 111 ASP cc_start: 0.7638 (t0) cc_final: 0.7395 (t70) REVERT: B 55 GLN cc_start: 0.8470 (tp40) cc_final: 0.8251 (tp-100) REVERT: B 111 ASP cc_start: 0.7706 (t0) cc_final: 0.7460 (t70) REVERT: C 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7457 (t70) REVERT: D 111 ASP cc_start: 0.7716 (t0) cc_final: 0.7485 (t70) REVERT: E 76 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7740 (p0) REVERT: E 111 ASP cc_start: 0.7691 (t0) cc_final: 0.7450 (t70) REVERT: F 111 ASP cc_start: 0.7690 (t0) cc_final: 0.7452 (t70) REVERT: G 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7479 (t70) REVERT: H 111 ASP cc_start: 0.7705 (t0) cc_final: 0.7464 (t70) REVERT: I 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7450 (t70) REVERT: J 111 ASP cc_start: 0.7686 (t0) cc_final: 0.7446 (t70) REVERT: K 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7477 (t70) REVERT: L 76 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7736 (p0) REVERT: L 111 ASP cc_start: 0.7670 (t0) cc_final: 0.7429 (t70) REVERT: M 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7439 (t70) REVERT: N 76 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7760 (p0) REVERT: N 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7437 (t70) REVERT: O 111 ASP cc_start: 0.7705 (t0) cc_final: 0.7466 (t70) REVERT: P 76 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7737 (p0) REVERT: P 111 ASP cc_start: 0.7667 (t0) cc_final: 0.7422 (t70) REVERT: Q 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7463 (t70) REVERT: R 76 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7735 (p0) REVERT: R 111 ASP cc_start: 0.7760 (t0) cc_final: 0.7525 (t70) REVERT: S 111 ASP cc_start: 0.7696 (t0) cc_final: 0.7455 (t70) REVERT: T 55 GLN cc_start: 0.8472 (tp40) cc_final: 0.8244 (tp-100) REVERT: T 111 ASP cc_start: 0.7686 (t0) cc_final: 0.7443 (t70) REVERT: U 111 ASP cc_start: 0.7697 (t0) cc_final: 0.7455 (t70) REVERT: V 55 GLN cc_start: 0.8485 (tp40) cc_final: 0.8255 (tp-100) REVERT: V 111 ASP cc_start: 0.7697 (t0) cc_final: 0.7457 (t70) REVERT: W 111 ASP cc_start: 0.7647 (t0) cc_final: 0.7403 (t70) REVERT: X 111 ASP cc_start: 0.7715 (t0) cc_final: 0.7472 (t70) outliers start: 30 outliers final: 6 residues processed: 348 average time/residue: 1.7882 time to fit residues: 733.0640 Evaluate side-chains 312 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 300 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain N 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 89 LYS 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 357 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 M 76 ASN O 76 ASN Q 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124732 restraints weight = 230674.909| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.33 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 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 = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33404 Z= 0.129 Angle : 0.393 3.216 45135 Z= 0.229 Chirality : 0.036 0.108 4897 Planarity : 0.003 0.033 5807 Dihedral : 3.612 12.234 4321 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.41 % Allowed : 12.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.12), residues: 3985 helix: 2.65 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.36 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 180 HIS 0.002 0.001 HIS R 36 PHE 0.005 0.001 PHE J 53 TYR 0.011 0.001 TYR I 126 ARG 0.001 0.000 ARG X 110 Details of bonding type rmsd hydrogen bonds : bond 0.06847 ( 2588) hydrogen bonds : angle 3.47104 ( 7785) covalent geometry : bond 0.00223 (33404) covalent geometry : angle 0.39260 (45135) *********************** 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 352 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 326 time to evaluate : 3.704 Fit side-chains REVERT: A 76 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 111 ASP cc_start: 0.7625 (t0) cc_final: 0.7403 (t70) REVERT: B 55 GLN cc_start: 0.8458 (tp40) cc_final: 0.8237 (tp-100) REVERT: B 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7439 (t70) REVERT: C 111 ASP cc_start: 0.7685 (t0) cc_final: 0.7446 (t70) REVERT: D 111 ASP cc_start: 0.7687 (t0) cc_final: 0.7455 (t70) REVERT: E 76 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7643 (p0) REVERT: E 111 ASP cc_start: 0.7666 (t0) cc_final: 0.7424 (t70) REVERT: F 111 ASP cc_start: 0.7682 (t0) cc_final: 0.7449 (t70) REVERT: G 111 ASP cc_start: 0.7685 (t0) cc_final: 0.7443 (t70) REVERT: H 55 GLN cc_start: 0.8447 (tp40) cc_final: 0.8223 (tp-100) REVERT: H 111 ASP cc_start: 0.7672 (t0) cc_final: 0.7434 (t70) REVERT: I 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7427 (t70) REVERT: J 111 ASP cc_start: 0.7664 (t0) cc_final: 0.7430 (t70) REVERT: K 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7445 (t70) REVERT: K 151 LYS cc_start: 0.7950 (pttm) cc_final: 0.7341 (mtmm) REVERT: L 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7424 (t70) REVERT: M 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7423 (t70) REVERT: N 111 ASP cc_start: 0.7652 (t0) cc_final: 0.7408 (t70) REVERT: O 111 ASP cc_start: 0.7689 (t0) cc_final: 0.7454 (t70) REVERT: P 111 ASP cc_start: 0.7637 (t0) cc_final: 0.7391 (t70) REVERT: Q 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7428 (t70) REVERT: R 111 ASP cc_start: 0.7705 (t0) cc_final: 0.7470 (t70) REVERT: S 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7431 (t70) REVERT: T 55 GLN cc_start: 0.8459 (tp40) cc_final: 0.8228 (tp-100) REVERT: T 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7419 (t70) REVERT: U 111 ASP cc_start: 0.7670 (t0) cc_final: 0.7430 (t70) REVERT: V 55 GLN cc_start: 0.8474 (tp40) cc_final: 0.8241 (tp-100) REVERT: V 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7434 (t70) REVERT: W 111 ASP cc_start: 0.7622 (t0) cc_final: 0.7381 (t70) REVERT: X 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7438 (t70) outliers start: 26 outliers final: 3 residues processed: 343 average time/residue: 1.5145 time to fit residues: 612.9147 Evaluate side-chains 313 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 308 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 363 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN H 76 ASN I 76 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126654 restraints weight = 235926.730| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.37 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33404 Z= 0.120 Angle : 0.381 3.107 45135 Z= 0.223 Chirality : 0.036 0.106 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.554 12.186 4321 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.18 % Allowed : 13.20 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.13), residues: 3985 helix: 2.77 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.11 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 180 HIS 0.002 0.001 HIS M 39 PHE 0.005 0.001 PHE J 53 TYR 0.010 0.001 TYR E 126 ARG 0.002 0.000 ARG T 75 Details of bonding type rmsd hydrogen bonds : bond 0.06332 ( 2588) hydrogen bonds : angle 3.40470 ( 7785) covalent geometry : bond 0.00197 (33404) covalent geometry : angle 0.38052 (45135) *********************** 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 357 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 339 time to evaluate : 3.334 Fit side-chains REVERT: A 111 ASP cc_start: 0.7614 (t0) cc_final: 0.7410 (t70) REVERT: B 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7439 (t70) REVERT: C 111 ASP cc_start: 0.7666 (t0) cc_final: 0.7455 (t70) REVERT: D 111 ASP cc_start: 0.7666 (t0) cc_final: 0.7464 (t70) REVERT: E 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7441 (t70) REVERT: F 111 ASP cc_start: 0.7653 (t0) cc_final: 0.7448 (t70) REVERT: G 111 ASP cc_start: 0.7665 (t0) cc_final: 0.7454 (t70) REVERT: H 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7447 (t70) REVERT: I 111 ASP cc_start: 0.7643 (t0) cc_final: 0.7431 (t70) REVERT: J 111 ASP cc_start: 0.7634 (t0) cc_final: 0.7424 (t70) REVERT: K 111 ASP cc_start: 0.7657 (t0) cc_final: 0.7450 (t70) REVERT: L 111 ASP cc_start: 0.7628 (t0) cc_final: 0.7416 (t70) REVERT: M 111 ASP cc_start: 0.7651 (t0) cc_final: 0.7441 (t70) REVERT: N 111 ASP cc_start: 0.7646 (t0) cc_final: 0.7430 (t70) REVERT: O 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7465 (t70) REVERT: P 111 ASP cc_start: 0.7624 (t0) cc_final: 0.7404 (t70) REVERT: Q 111 ASP cc_start: 0.7649 (t0) cc_final: 0.7437 (t70) REVERT: R 111 ASP cc_start: 0.7686 (t0) cc_final: 0.7485 (t70) REVERT: S 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7444 (t70) REVERT: T 111 ASP cc_start: 0.7630 (t0) cc_final: 0.7411 (t70) REVERT: U 111 ASP cc_start: 0.7646 (t0) cc_final: 0.7437 (t70) REVERT: V 111 ASP cc_start: 0.7663 (t0) cc_final: 0.7450 (t70) REVERT: W 111 ASP cc_start: 0.7613 (t0) cc_final: 0.7398 (t70) REVERT: X 111 ASP cc_start: 0.7659 (t0) cc_final: 0.7449 (t70) outliers start: 18 outliers final: 3 residues processed: 353 average time/residue: 1.4137 time to fit residues: 590.7487 Evaluate side-chains 326 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 323 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain V residue 76 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 327 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 358 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 383 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 355 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 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 = 0.3687 r_free = 0.3687 target = 0.144800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121981 restraints weight = 231917.612| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.27 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1954 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= 0.148 Angle : 0.418 3.411 45135 Z= 0.244 Chirality : 0.037 0.114 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.650 12.072 4321 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.51 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.12), residues: 3985 helix: 2.56 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.00 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 180 HIS 0.003 0.001 HIS U 36 PHE 0.006 0.001 PHE A 153 TYR 0.012 0.002 TYR R 126 ARG 0.002 0.000 ARG V 75 Details of bonding type rmsd hydrogen bonds : bond 0.07794 ( 2588) hydrogen bonds : angle 3.60768 ( 7785) covalent geometry : bond 0.00271 (33404) covalent geometry : angle 0.41786 (45135) *********************** 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 356 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 4.000 Fit side-chains REVERT: A 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7453 (t70) REVERT: A 151 LYS cc_start: 0.7976 (pttm) cc_final: 0.7376 (mtmm) REVERT: B 55 GLN cc_start: 0.8460 (tp40) cc_final: 0.8233 (tp-100) REVERT: B 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7451 (t70) REVERT: B 151 LYS cc_start: 0.7957 (pttm) cc_final: 0.7345 (mtmm) REVERT: C 111 ASP cc_start: 0.7698 (t0) cc_final: 0.7484 (t70) REVERT: C 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7378 (mtmm) REVERT: D 111 ASP cc_start: 0.7697 (t0) cc_final: 0.7491 (t70) REVERT: D 151 LYS cc_start: 0.7977 (pttm) cc_final: 0.7378 (mtmm) REVERT: E 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7461 (t70) REVERT: E 151 LYS cc_start: 0.8014 (pttm) cc_final: 0.7421 (mtmm) REVERT: F 111 ASP cc_start: 0.7697 (t0) cc_final: 0.7488 (t70) REVERT: F 151 LYS cc_start: 0.7969 (pttm) cc_final: 0.7363 (mtmm) REVERT: G 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7482 (t70) REVERT: H 55 GLN cc_start: 0.8465 (tp40) cc_final: 0.8235 (tp-100) REVERT: H 111 ASP cc_start: 0.7700 (t0) cc_final: 0.7483 (t70) REVERT: H 151 LYS cc_start: 0.7999 (pttm) cc_final: 0.7408 (mtmm) REVERT: I 111 ASP cc_start: 0.7680 (t0) cc_final: 0.7465 (t70) REVERT: I 151 LYS cc_start: 0.7996 (pttm) cc_final: 0.7385 (mtmm) REVERT: J 111 ASP cc_start: 0.7678 (t0) cc_final: 0.7464 (t70) REVERT: J 151 LYS cc_start: 0.7967 (pttm) cc_final: 0.7393 (mtmm) REVERT: K 111 ASP cc_start: 0.7695 (t0) cc_final: 0.7481 (t70) REVERT: K 151 LYS cc_start: 0.7994 (pttm) cc_final: 0.7399 (mtmm) REVERT: L 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7467 (t70) REVERT: M 111 ASP cc_start: 0.7670 (t0) cc_final: 0.7456 (t70) REVERT: M 151 LYS cc_start: 0.7992 (pttm) cc_final: 0.7389 (mtmm) REVERT: N 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7444 (t70) REVERT: N 151 LYS cc_start: 0.7984 (pttm) cc_final: 0.7387 (mtmm) REVERT: O 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7492 (t70) REVERT: O 151 LYS cc_start: 0.7976 (pttm) cc_final: 0.7367 (mtmm) REVERT: P 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7448 (t70) REVERT: P 151 LYS cc_start: 0.7982 (pttm) cc_final: 0.7415 (mtmm) REVERT: Q 111 ASP cc_start: 0.7685 (t0) cc_final: 0.7472 (t70) REVERT: Q 151 LYS cc_start: 0.7970 (pttm) cc_final: 0.7367 (mtmm) REVERT: R 111 ASP cc_start: 0.7714 (t0) cc_final: 0.7500 (t70) REVERT: R 151 LYS cc_start: 0.7961 (pttm) cc_final: 0.7391 (mtmm) REVERT: S 111 ASP cc_start: 0.7684 (t0) cc_final: 0.7468 (t70) REVERT: S 151 LYS cc_start: 0.7976 (pttm) cc_final: 0.7379 (mtmm) REVERT: T 55 GLN cc_start: 0.8487 (tp40) cc_final: 0.8249 (tp-100) REVERT: T 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7436 (t70) REVERT: T 151 LYS cc_start: 0.7980 (pttm) cc_final: 0.7378 (mtmm) REVERT: U 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7464 (t70) REVERT: V 55 GLN cc_start: 0.8476 (tp40) cc_final: 0.8238 (tp-100) REVERT: V 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7457 (t70) REVERT: V 151 LYS cc_start: 0.8005 (pttm) cc_final: 0.7405 (mtmm) REVERT: W 111 ASP cc_start: 0.7633 (t0) cc_final: 0.7415 (t70) REVERT: W 151 LYS cc_start: 0.7984 (pttm) cc_final: 0.7383 (mtmm) REVERT: X 111 ASP cc_start: 0.7705 (t0) cc_final: 0.7493 (t70) REVERT: X 151 LYS cc_start: 0.8010 (pttm) cc_final: 0.7406 (mtmm) outliers start: 24 outliers final: 11 residues processed: 356 average time/residue: 1.5738 time to fit residues: 654.8183 Evaluate side-chains 324 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 313 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain I 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 O 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 W 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 1 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 327 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.138983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116589 restraints weight = 227902.641| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.10 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33404 Z= 0.199 Angle : 0.490 3.653 45135 Z= 0.282 Chirality : 0.040 0.123 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.885 13.641 4321 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.38 % Allowed : 13.68 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.12), residues: 3985 helix: 2.26 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -1.12 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 180 HIS 0.003 0.001 HIS Q 56 PHE 0.009 0.002 PHE A 153 TYR 0.017 0.002 TYR K 126 ARG 0.001 0.000 ARG T 137 Details of bonding type rmsd hydrogen bonds : bond 0.09877 ( 2588) hydrogen bonds : angle 3.87440 ( 7785) covalent geometry : bond 0.00413 (33404) covalent geometry : angle 0.49041 (45135) *********************** 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 338 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 3.770 Fit side-chains REVERT: A 151 LYS cc_start: 0.8300 (pttm) cc_final: 0.7720 (mtmm) REVERT: B 55 GLN cc_start: 0.8482 (tp40) cc_final: 0.8273 (tp-100) REVERT: B 151 LYS cc_start: 0.8287 (pttm) cc_final: 0.7702 (mtmm) REVERT: C 151 LYS cc_start: 0.8301 (pttm) cc_final: 0.7710 (mtmm) REVERT: D 151 LYS cc_start: 0.8306 (pttm) cc_final: 0.7727 (mtmm) REVERT: E 151 LYS cc_start: 0.8286 (pttm) cc_final: 0.7701 (mtmm) REVERT: F 151 LYS cc_start: 0.8302 (pttm) cc_final: 0.7726 (mtmm) REVERT: G 151 LYS cc_start: 0.8198 (pttm) cc_final: 0.7575 (mtmt) REVERT: H 55 GLN cc_start: 0.8463 (tp40) cc_final: 0.8251 (tp-100) REVERT: H 151 LYS cc_start: 0.8316 (pttm) cc_final: 0.7743 (mtmm) REVERT: I 151 LYS cc_start: 0.8205 (pttm) cc_final: 0.7583 (mtmm) REVERT: J 151 LYS cc_start: 0.8319 (pttm) cc_final: 0.7749 (mtmm) REVERT: K 151 LYS cc_start: 0.8302 (pttm) cc_final: 0.7722 (mtmm) REVERT: L 151 LYS cc_start: 0.8300 (pttm) cc_final: 0.7716 (mtmm) REVERT: M 151 LYS cc_start: 0.8301 (pttm) cc_final: 0.7717 (mtmm) REVERT: N 151 LYS cc_start: 0.8308 (pttm) cc_final: 0.7728 (mtmm) REVERT: O 151 LYS cc_start: 0.8190 (pttm) cc_final: 0.7576 (mtmm) REVERT: P 151 LYS cc_start: 0.8306 (pttm) cc_final: 0.7731 (mtmm) REVERT: Q 151 LYS cc_start: 0.8287 (pttm) cc_final: 0.7702 (mtmm) REVERT: R 151 LYS cc_start: 0.8296 (pttm) cc_final: 0.7713 (mtmm) REVERT: S 151 LYS cc_start: 0.8307 (pttm) cc_final: 0.7733 (mtmm) REVERT: T 55 GLN cc_start: 0.8493 (tp40) cc_final: 0.8279 (tp-100) REVERT: T 151 LYS cc_start: 0.8302 (pttm) cc_final: 0.7714 (mtmm) REVERT: U 151 LYS cc_start: 0.8307 (pttm) cc_final: 0.7730 (mtmm) REVERT: V 55 GLN cc_start: 0.8482 (tp40) cc_final: 0.8259 (tp-100) REVERT: V 151 LYS cc_start: 0.8290 (pttm) cc_final: 0.7702 (mtmm) REVERT: W 151 LYS cc_start: 0.8286 (pttm) cc_final: 0.7703 (mtmm) REVERT: X 151 LYS cc_start: 0.8225 (pttm) cc_final: 0.7616 (mtmm) outliers start: 24 outliers final: 4 residues processed: 332 average time/residue: 1.7667 time to fit residues: 686.9197 Evaluate side-chains 290 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 286 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain K 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 106 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 370 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 335 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.145944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123210 restraints weight = 232647.196| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.21 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1955 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= 0.138 Angle : 0.416 3.534 45135 Z= 0.244 Chirality : 0.036 0.114 4897 Planarity : 0.003 0.033 5807 Dihedral : 3.708 12.431 4321 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer: Outliers : 1.35 % Allowed : 13.09 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.12), residues: 3985 helix: 2.54 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.90 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS O 39 PHE 0.008 0.001 PHE A 73 TYR 0.011 0.001 TYR B 126 ARG 0.006 0.000 ARG K 75 Details of bonding type rmsd hydrogen bonds : bond 0.07348 ( 2588) hydrogen bonds : angle 3.60028 ( 7785) covalent geometry : bond 0.00241 (33404) covalent geometry : angle 0.41577 (45135) ********************** 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 343 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 3.557 Fit side-chains REVERT: A 111 ASP cc_start: 0.7703 (t0) cc_final: 0.7405 (t70) REVERT: A 151 LYS cc_start: 0.8051 (pttm) cc_final: 0.7475 (mtmm) REVERT: B 55 GLN cc_start: 0.8483 (tp40) cc_final: 0.8260 (tp-100) REVERT: B 111 ASP cc_start: 0.7696 (t0) cc_final: 0.7388 (t70) REVERT: B 151 LYS cc_start: 0.8014 (pttm) cc_final: 0.7418 (mtmm) REVERT: C 111 ASP cc_start: 0.7718 (t0) cc_final: 0.7408 (t70) REVERT: D 111 ASP cc_start: 0.7723 (t0) cc_final: 0.7432 (t70) REVERT: D 151 LYS cc_start: 0.8037 (pttm) cc_final: 0.7451 (mtmm) REVERT: E 111 ASP cc_start: 0.7695 (t0) cc_final: 0.7386 (t70) REVERT: E 151 LYS cc_start: 0.8044 (pttm) cc_final: 0.7463 (mtmm) REVERT: F 111 ASP cc_start: 0.7724 (t0) cc_final: 0.7425 (t70) REVERT: F 151 LYS cc_start: 0.8028 (pttm) cc_final: 0.7444 (mtmm) REVERT: G 111 ASP cc_start: 0.7708 (t0) cc_final: 0.7398 (t70) REVERT: H 55 GLN cc_start: 0.8486 (tp40) cc_final: 0.8261 (tp-100) REVERT: H 111 ASP cc_start: 0.7716 (t0) cc_final: 0.7414 (t70) REVERT: H 151 LYS cc_start: 0.8050 (pttm) cc_final: 0.7476 (mtmm) REVERT: I 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7385 (t70) REVERT: I 151 LYS cc_start: 0.8040 (pttm) cc_final: 0.7442 (mtmm) REVERT: J 111 ASP cc_start: 0.7677 (t0) cc_final: 0.7372 (t70) REVERT: J 151 LYS cc_start: 0.8049 (pttm) cc_final: 0.7478 (mtmm) REVERT: K 111 ASP cc_start: 0.7727 (t0) cc_final: 0.7431 (t70) REVERT: K 151 LYS cc_start: 0.8049 (pttm) cc_final: 0.7472 (mtmm) REVERT: L 111 ASP cc_start: 0.7695 (t0) cc_final: 0.7386 (t70) REVERT: M 111 ASP cc_start: 0.7698 (t0) cc_final: 0.7392 (t70) REVERT: M 151 LYS cc_start: 0.8038 (pttm) cc_final: 0.7451 (mtmm) REVERT: N 111 ASP cc_start: 0.7672 (t0) cc_final: 0.7362 (t70) REVERT: N 151 LYS cc_start: 0.8048 (pttm) cc_final: 0.7473 (mtmm) REVERT: O 111 ASP cc_start: 0.7732 (t0) cc_final: 0.7430 (t70) REVERT: O 151 LYS cc_start: 0.8012 (pttm) cc_final: 0.7417 (mtmm) REVERT: P 111 ASP cc_start: 0.7684 (t0) cc_final: 0.7376 (t70) REVERT: P 151 LYS cc_start: 0.8051 (pttm) cc_final: 0.7478 (mtmm) REVERT: Q 111 ASP cc_start: 0.7709 (t0) cc_final: 0.7404 (t70) REVERT: Q 151 LYS cc_start: 0.8035 (pttm) cc_final: 0.7450 (mtmm) REVERT: R 111 ASP cc_start: 0.7747 (t0) cc_final: 0.7452 (t70) REVERT: R 151 LYS cc_start: 0.8042 (pttm) cc_final: 0.7468 (mtmm) REVERT: S 111 ASP cc_start: 0.7700 (t0) cc_final: 0.7395 (t70) REVERT: S 151 LYS cc_start: 0.8043 (pttm) cc_final: 0.7464 (mtmm) REVERT: T 55 GLN cc_start: 0.8501 (tp40) cc_final: 0.8270 (tp-100) REVERT: T 111 ASP cc_start: 0.7662 (t0) cc_final: 0.7354 (t70) REVERT: T 151 LYS cc_start: 0.8049 (pttm) cc_final: 0.7461 (mtmm) REVERT: U 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7419 (t70) REVERT: V 55 GLN cc_start: 0.8495 (tp40) cc_final: 0.8262 (tp-100) REVERT: V 111 ASP cc_start: 0.7681 (t0) cc_final: 0.7372 (t70) REVERT: V 151 LYS cc_start: 0.8031 (pttm) cc_final: 0.7440 (mtmm) REVERT: W 111 ASP cc_start: 0.7650 (t0) cc_final: 0.7340 (t70) REVERT: W 151 LYS cc_start: 0.8023 (pttm) cc_final: 0.7433 (mtmm) REVERT: X 111 ASP cc_start: 0.7730 (t0) cc_final: 0.7430 (t70) REVERT: X 151 LYS cc_start: 0.8054 (pttm) cc_final: 0.7467 (mtmm) outliers start: 24 outliers final: 5 residues processed: 339 average time/residue: 1.6847 time to fit residues: 662.6571 Evaluate side-chains 309 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 304 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain M 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 333 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 342 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 381 optimal weight: 10.0000 chunk 8 optimal weight: 0.0270 chunk 325 optimal weight: 3.9990 overall best weight: 3.1844 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.140670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118145 restraints weight = 219160.231| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.12 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33404 Z= 0.189 Angle : 0.477 4.277 45135 Z= 0.274 Chirality : 0.040 0.123 4897 Planarity : 0.003 0.033 5807 Dihedral : 3.820 12.654 4321 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.71 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.12), residues: 3985 helix: 2.27 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -1.01 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP Q 180 HIS 0.003 0.001 HIS N 39 PHE 0.009 0.002 PHE A 153 TYR 0.015 0.002 TYR K 126 ARG 0.005 0.000 ARG M 75 Details of bonding type rmsd hydrogen bonds : bond 0.09151 ( 2588) hydrogen bonds : angle 3.77353 ( 7785) covalent geometry : bond 0.00395 (33404) covalent geometry : angle 0.47701 (45135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17716.95 seconds wall clock time: 308 minutes 7.90 seconds (18487.90 seconds total)