Starting phenix.real_space_refine on Mon Jul 6 01:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqu_37754/07_2026/8wqu_37754.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.151 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 5328 2.21 5 O 6384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32736 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: 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: "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: 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: "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: 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: "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: 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: "P" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "Q" Number of atoms: 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: 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: "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: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 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: 11.48, per 1000 atoms: 0.35 Number of scatterers: 32736 At special positions: 0 Unit cell: (132.956, 132.956, 132.956, 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 6384 8.00 N 5328 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: 2.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 12 sheets defined 82.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.663A pdb=" N ASN A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 3.530A pdb=" N PHE A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 132 through 151 removed outlier: 4.019A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'C' and resid 14 through 45 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.525A pdb=" N PHE C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.527A pdb=" N PHE D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 3.542A pdb=" N PHE G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.958A 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 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 122 removed outlier: 3.783A pdb=" N LEU H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 151 removed outlier: 4.016A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 45 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 122 removed outlier: 3.784A pdb=" N LEU K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'L' and resid 14 through 45 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 122 removed outlier: 3.675A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'M' and resid 14 through 45 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 151 removed outlier: 4.263A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 122 removed outlier: 3.674A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 171 Processing helix chain 'O' and resid 14 through 45 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 122 removed outlier: 3.787A pdb=" N LEU O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 151 removed outlier: 4.624A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 155 Processing helix chain 'P' and resid 158 through 171 Processing helix chain 'Q' and resid 14 through 45 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 3.517A pdb=" N PHE Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 155 Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 122 removed outlier: 3.679A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'S' and resid 14 through 45 Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.551A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR S 130 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 151 removed outlier: 4.024A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 Processing helix chain 'T' and resid 158 through 171 Processing helix chain 'U' and resid 14 through 45 Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 151 removed outlier: 4.369A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 171 Processing helix chain 'W' and resid 14 through 45 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 155 Processing helix chain 'W' and resid 158 through 171 Processing helix chain 'X' and resid 14 through 45 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.474A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 122 removed outlier: 3.788A pdb=" N LEU X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 151 removed outlier: 4.625A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 155 Processing helix chain 'X' and resid 158 through 171 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 2550 hydrogen bonds defined for protein. 7626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5856 1.28 - 1.41: 8442 1.41 - 1.54: 18870 1.54 - 1.67: 96 1.67 - 1.81: 144 Bond restraints: 33408 Sorted by residual: bond pdb=" C PHE I 129 " pdb=" O PHE I 129 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.31e-02 5.83e+03 4.60e+01 bond pdb=" C PHE E 129 " pdb=" O PHE E 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE O 129 " pdb=" O PHE O 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE N 129 " pdb=" O PHE N 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 bond pdb=" C PHE F 129 " pdb=" O PHE F 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 ... (remaining 33403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 43569 1.63 - 3.26: 1207 3.26 - 4.90: 239 4.90 - 6.53: 67 6.53 - 8.16: 62 Bond angle restraints: 45144 Sorted by residual: angle pdb=" N TYR A 126 " pdb=" CA TYR A 126 " pdb=" C TYR A 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR Q 126 " pdb=" CA TYR Q 126 " pdb=" C TYR Q 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR D 126 " pdb=" CA TYR D 126 " pdb=" C TYR D 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR C 126 " pdb=" CA TYR C 126 " pdb=" C TYR C 126 " ideal model delta sigma weight residual 113.17 105.21 7.96 1.26e+00 6.30e-01 3.99e+01 angle pdb=" N TYR T 126 " pdb=" CA TYR T 126 " pdb=" C TYR T 126 " ideal model delta sigma weight residual 113.17 105.24 7.93 1.26e+00 6.30e-01 3.96e+01 ... (remaining 45139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17913 16.60 - 33.20: 1699 33.20 - 49.80: 247 49.80 - 66.40: 114 66.40 - 83.00: 67 Dihedral angle restraints: 20040 sinusoidal: 8136 harmonic: 11904 Sorted by residual: dihedral pdb=" C ASP A 124 " pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" CB ASP A 124 " ideal model delta harmonic sigma weight residual -122.60 -139.62 17.02 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C ASP C 124 " pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " ideal model delta harmonic sigma weight residual -122.60 -139.60 17.00 0 2.50e+00 1.60e-01 4.62e+01 dihedral pdb=" C ASP D 124 " pdb=" N ASP D 124 " pdb=" CA ASP D 124 " pdb=" CB ASP D 124 " ideal model delta harmonic sigma weight residual -122.60 -139.59 16.99 0 2.50e+00 1.60e-01 4.62e+01 ... (remaining 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4849 0.168 - 0.336: 23 0.336 - 0.504: 0 0.504 - 0.673: 16 0.673 - 0.841: 8 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA ASP U 124 " pdb=" N ASP U 124 " pdb=" C ASP U 124 " pdb=" CB ASP U 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP A 124 " pdb=" N ASP A 124 " pdb=" C ASP A 124 " pdb=" CB ASP A 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP C 124 " pdb=" N ASP C 124 " pdb=" C ASP C 124 " pdb=" CB ASP C 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 4893 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 123 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLU F 123 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU F 123 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU P 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU P 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP P 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU G 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU G 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP G 124 " -0.023 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 27842 3.20 - 3.77: 48410 3.77 - 4.33: 68676 4.33 - 4.90: 114527 Nonbonded interactions: 259623 Sorted by model distance: nonbonded pdb=" NE2 HIS E 65 " pdb="FE FE E 201 " model vdw 2.074 3.080 nonbonded pdb=" NE2 HIS L 65 " pdb="FE FE L 201 " model vdw 2.074 3.080 nonbonded pdb=" NE2 HIS A 65 " pdb="FE FE A 201 " model vdw 2.074 3.080 nonbonded pdb=" NE2 HIS G 65 " pdb="FE FE G 201 " model vdw 2.074 3.080 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.074 3.080 ... (remaining 259618 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 33.620 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.010 0.089 33408 Z= 0.569 Angle : 0.750 8.160 45144 Z= 0.453 Chirality : 0.066 0.841 4896 Planarity : 0.005 0.041 5808 Dihedral : 14.543 82.999 12360 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 3984 helix: 0.10 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -2.65 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 110 TYR 0.033 0.004 TYR M 130 PHE 0.015 0.002 PHE I 129 TRP 0.004 0.002 TRP L 180 HIS 0.005 0.001 HIS G 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00951 / 0.57 (33408) covalent geometry : angle 0.74959 / 0.45 (45144) hydrogen bonds : bond 0.15897 / 10.41 ( 2550) hydrogen bonds : angle 5.66229 / 4.05 ( 7626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 1.232 Fit side-chains REVERT: A 76 ASN cc_start: 0.8166 (p0) cc_final: 0.7507 (p0) REVERT: A 114 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7548 (tttt) REVERT: B 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7407 (p0) REVERT: B 114 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7548 (tttt) REVERT: C 76 ASN cc_start: 0.8077 (p0) cc_final: 0.7413 (p0) REVERT: C 114 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7529 (tttt) REVERT: D 76 ASN cc_start: 0.8169 (p0) cc_final: 0.7533 (p0) REVERT: D 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7521 (tttt) REVERT: E 76 ASN cc_start: 0.8057 (p0) cc_final: 0.7386 (p0) REVERT: F 76 ASN cc_start: 0.8032 (p0) cc_final: 0.7357 (p0) REVERT: F 114 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7534 (tttt) REVERT: G 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: G 114 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7514 (tttt) REVERT: H 76 ASN cc_start: 0.8073 (p0) cc_final: 0.7404 (p0) REVERT: H 114 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7527 (tttt) REVERT: I 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: I 114 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7556 (tttt) REVERT: J 76 ASN cc_start: 0.8087 (p0) cc_final: 0.7422 (p0) REVERT: J 114 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7525 (tttt) REVERT: K 76 ASN cc_start: 0.8090 (p0) cc_final: 0.7418 (p0) REVERT: K 114 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7577 (tttt) REVERT: L 76 ASN cc_start: 0.8059 (p0) cc_final: 0.7398 (p0) REVERT: L 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7539 (tttt) REVERT: M 76 ASN cc_start: 0.8046 (p0) cc_final: 0.7368 (p0) REVERT: M 114 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7533 (tttt) REVERT: N 76 ASN cc_start: 0.8156 (p0) cc_final: 0.7494 (p0) REVERT: N 114 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7553 (tttt) REVERT: O 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7384 (p0) REVERT: O 114 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7547 (tttt) REVERT: P 76 ASN cc_start: 0.8052 (p0) cc_final: 0.7374 (p0) REVERT: P 114 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7522 (tttt) REVERT: Q 76 ASN cc_start: 0.8045 (p0) cc_final: 0.7371 (p0) REVERT: Q 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7552 (tttt) REVERT: R 76 ASN cc_start: 0.8033 (p0) cc_final: 0.7359 (p0) REVERT: R 114 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7589 (tttt) REVERT: S 76 ASN cc_start: 0.8181 (p0) cc_final: 0.7523 (p0) REVERT: S 114 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7524 (tttt) REVERT: T 76 ASN cc_start: 0.8083 (p0) cc_final: 0.7417 (p0) REVERT: T 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7523 (tttt) REVERT: U 76 ASN cc_start: 0.8047 (p0) cc_final: 0.7364 (p0) REVERT: U 114 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7527 (tttt) REVERT: V 76 ASN cc_start: 0.8067 (p0) cc_final: 0.7404 (p0) REVERT: V 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7543 (tttt) REVERT: W 76 ASN cc_start: 0.8148 (p0) cc_final: 0.7480 (p0) REVERT: W 114 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7556 (tttt) REVERT: X 76 ASN cc_start: 0.8052 (p0) cc_final: 0.7380 (p0) REVERT: X 114 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7531 (tttt) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.5760 time to fit residues: 365.3760 Evaluate side-chains 309 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN B 22 GLN C 22 GLN D 22 GLN E 22 GLN F 22 GLN G 22 GLN H 22 GLN I 22 GLN J 22 GLN K 22 GLN M 22 GLN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN S 22 GLN T 22 GLN U 22 GLN V 22 GLN W 22 GLN X 22 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127610 restraints weight = 198127.386| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.39 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 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 = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33408 Z= 0.136 Angle : 0.451 4.363 45144 Z= 0.255 Chirality : 0.036 0.113 4896 Planarity : 0.004 0.039 5808 Dihedral : 3.953 11.961 4320 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.42 % Allowed : 6.14 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.13), residues: 3984 helix: 1.69 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.72 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 105 TYR 0.017 0.001 TYR D 24 PHE 0.013 0.001 PHE U 129 TRP 0.002 0.001 TRP V 134 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (33408) covalent geometry : angle 0.45127 / 0.26 (45144) hydrogen bonds : bond 0.06983 / 4.69 ( 2550) hydrogen bonds : angle 3.95854 / 2.86 ( 7626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 449 time to evaluate : 0.926 Fit side-chains REVERT: A 60 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: A 107 ASN cc_start: 0.8917 (t0) cc_final: 0.8626 (t0) REVERT: A 114 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7702 (tttt) REVERT: B 114 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7694 (tttt) REVERT: C 114 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7707 (tttt) REVERT: D 60 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: D 107 ASN cc_start: 0.8913 (t0) cc_final: 0.8619 (t0) REVERT: D 114 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7706 (tttt) REVERT: E 60 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: E 114 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7713 (tttt) REVERT: F 60 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: F 114 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7715 (tttt) REVERT: G 114 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7703 (tttt) REVERT: H 114 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7701 (tttt) REVERT: I 60 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: I 107 ASN cc_start: 0.8911 (t0) cc_final: 0.8625 (t0) REVERT: I 114 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7701 (tttt) REVERT: J 114 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7721 (tttt) REVERT: K 107 ASN cc_start: 0.8916 (t0) cc_final: 0.8618 (t0) REVERT: K 114 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7656 (tttt) REVERT: L 60 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: L 107 ASN cc_start: 0.8909 (t0) cc_final: 0.8618 (t0) REVERT: L 114 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7676 (tttt) REVERT: M 60 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: M 107 ASN cc_start: 0.8905 (t0) cc_final: 0.8611 (t0) REVERT: M 114 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7718 (tttt) REVERT: N 60 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: N 107 ASN cc_start: 0.8907 (t0) cc_final: 0.8618 (t0) REVERT: N 114 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7714 (tttt) REVERT: O 114 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7702 (tttt) REVERT: P 114 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7708 (tttt) REVERT: Q 60 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: Q 107 ASN cc_start: 0.8903 (t0) cc_final: 0.8620 (t0) REVERT: Q 114 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7716 (tttt) REVERT: R 60 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: R 107 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8592 (t0) REVERT: R 114 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7731 (tttt) REVERT: S 60 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: S 107 ASN cc_start: 0.8918 (t0) cc_final: 0.8626 (t0) REVERT: S 114 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7722 (tttt) REVERT: T 114 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7727 (tttt) REVERT: U 60 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: U 107 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8583 (t0) REVERT: U 114 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7679 (tttt) REVERT: V 114 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7696 (tttt) REVERT: W 60 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: W 107 ASN cc_start: 0.8907 (t0) cc_final: 0.8622 (t0) REVERT: W 114 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7711 (tttt) REVERT: X 114 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7708 (tttt) outliers start: 15 outliers final: 0 residues processed: 464 average time/residue: 0.5487 time to fit residues: 313.8749 Evaluate side-chains 366 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 351 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 196 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 377 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 329 optimal weight: 5.9990 chunk 367 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123625 restraints weight = 213317.410| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.46 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33408 Z= 0.156 Angle : 0.462 5.517 45144 Z= 0.259 Chirality : 0.037 0.113 4896 Planarity : 0.003 0.039 5808 Dihedral : 3.818 11.964 4320 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.35 % Allowed : 8.90 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.13), residues: 3984 helix: 2.00 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.39 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 110 TYR 0.016 0.002 TYR D 24 PHE 0.011 0.001 PHE N 129 TRP 0.002 0.001 TRP R 180 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (33408) covalent geometry : angle 0.46191 / 0.26 (45144) hydrogen bonds : bond 0.08039 / 5.38 ( 2550) hydrogen bonds : angle 3.88084 / 2.81 ( 7626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 399 time to evaluate : 1.346 Fit side-chains REVERT: A 60 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: D 60 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: E 60 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: F 60 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: I 60 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: I 114 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7814 (tttt) REVERT: L 60 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: M 60 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: N 60 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: Q 60 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: R 60 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: R 107 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8500 (t0) REVERT: S 60 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: U 60 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: U 107 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8496 (t0) REVERT: W 60 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7183 (m-30) outliers start: 39 outliers final: 24 residues processed: 414 average time/residue: 0.5598 time to fit residues: 287.3591 Evaluate side-chains 377 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 84 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126430 restraints weight = 201233.170| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.25 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33408 Z= 0.130 Angle : 0.425 5.479 45144 Z= 0.238 Chirality : 0.036 0.113 4896 Planarity : 0.003 0.037 5808 Dihedral : 3.667 12.301 4320 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.67 % Allowed : 9.23 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.13), residues: 3984 helix: 2.34 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.08 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 110 TYR 0.015 0.001 TYR D 24 PHE 0.010 0.001 PHE U 129 TRP 0.002 0.001 TRP A 180 HIS 0.005 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (33408) covalent geometry : angle 0.42487 / 0.24 (45144) hydrogen bonds : bond 0.06984 / 4.68 ( 2550) hydrogen bonds : angle 3.71686 / 2.69 ( 7626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 360 time to evaluate : 1.289 Fit side-chains REVERT: A 60 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: B 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 107 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (t0) REVERT: D 60 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: E 60 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: F 60 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: F 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8419 (t0) REVERT: I 60 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: L 60 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: M 60 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: N 60 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: O 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8429 (t0) REVERT: P 107 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8446 (t0) REVERT: Q 60 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: R 60 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: R 107 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8418 (t0) REVERT: S 60 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: T 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8439 (t0) REVERT: U 60 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7122 (m-30) REVERT: U 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8412 (t0) REVERT: W 60 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: X 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8434 (t0) outliers start: 78 outliers final: 0 residues processed: 391 average time/residue: 0.4608 time to fit residues: 227.7596 Evaluate side-chains 366 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 344 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 188 optimal weight: 0.9980 chunk 238 optimal weight: 9.9990 chunk 381 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 246 optimal weight: 0.0980 chunk 186 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130388 restraints weight = 198583.058| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.35 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33408 Z= 0.116 Angle : 0.400 5.782 45144 Z= 0.223 Chirality : 0.036 0.113 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.538 12.163 4320 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.42 % Allowed : 9.85 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.81 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 110 TYR 0.014 0.001 TYR D 24 PHE 0.009 0.001 PHE N 129 TRP 0.002 0.000 TRP A 180 HIS 0.005 0.001 HIS U 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.12 (33408) covalent geometry : angle 0.39967 / 0.22 (45144) hydrogen bonds : bond 0.06128 / 4.11 ( 2550) hydrogen bonds : angle 3.58036 / 2.59 ( 7626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 348 time to evaluate : 1.342 Fit side-chains REVERT: A 60 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: A 107 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8564 (t0) REVERT: B 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (t0) REVERT: C 107 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (t0) REVERT: D 60 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: D 107 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8535 (t0) REVERT: E 60 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: E 107 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8559 (t0) REVERT: F 60 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: F 107 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8536 (t0) REVERT: G 107 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8534 (t0) REVERT: I 60 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: I 107 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8556 (t0) REVERT: J 107 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8523 (t0) REVERT: K 107 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8546 (t0) REVERT: L 60 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: L 107 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8556 (t0) REVERT: M 60 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: M 107 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8549 (t0) REVERT: N 60 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: N 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8536 (t0) REVERT: O 107 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8527 (t0) REVERT: P 107 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8539 (t0) REVERT: Q 60 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: Q 107 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8543 (t0) REVERT: R 60 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: R 107 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8538 (t0) REVERT: S 60 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: S 107 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (t0) REVERT: T 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8542 (t0) REVERT: U 60 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: U 107 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8534 (t0) REVERT: V 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8572 (t0) REVERT: W 60 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: W 107 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8556 (t0) REVERT: X 107 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8544 (t0) outliers start: 65 outliers final: 0 residues processed: 388 average time/residue: 0.4660 time to fit residues: 232.1653 Evaluate side-chains 357 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 381 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 371 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127062 restraints weight = 197778.351| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.43 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 33408 Z= 0.127 Angle : 0.410 5.900 45144 Z= 0.230 Chirality : 0.036 0.122 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.553 12.539 4320 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.03 % Allowed : 11.01 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.71 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 110 TYR 0.014 0.001 TYR G 24 PHE 0.010 0.001 PHE N 129 TRP 0.002 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (33408) covalent geometry : angle 0.40998 / 0.23 (45144) hydrogen bonds : bond 0.06713 / 4.50 ( 2550) hydrogen bonds : angle 3.66237 / 2.65 ( 7626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 1.312 Fit side-chains REVERT: A 60 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: A 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8476 (t0) REVERT: B 107 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8491 (t0) REVERT: C 107 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (t0) REVERT: D 60 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: D 107 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8452 (t0) REVERT: E 60 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: E 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8458 (t0) REVERT: F 60 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: F 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (t0) REVERT: G 107 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (t0) REVERT: H 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8468 (t0) REVERT: I 60 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: I 107 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8460 (t0) REVERT: J 107 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8474 (t0) REVERT: K 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (t0) REVERT: L 60 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: L 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8466 (t0) REVERT: M 60 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: M 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8463 (t0) REVERT: N 60 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: N 107 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8441 (t0) REVERT: O 107 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8482 (t0) REVERT: P 107 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8483 (t0) REVERT: Q 60 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: Q 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8464 (t0) REVERT: R 60 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: R 107 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8449 (t0) REVERT: S 60 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: S 107 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (t0) REVERT: T 107 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8498 (t0) REVERT: U 60 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: U 107 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8487 (t0) REVERT: V 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8479 (t0) REVERT: W 60 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: W 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8460 (t0) REVERT: X 107 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8486 (t0) outliers start: 49 outliers final: 0 residues processed: 370 average time/residue: 0.4290 time to fit residues: 207.0587 Evaluate side-chains 359 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 322 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 319 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 358 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 348 optimal weight: 0.9990 chunk 333 optimal weight: 0.9980 chunk 296 optimal weight: 0.1980 chunk 287 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133664 restraints weight = 209836.078| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.58 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 33408 Z= 0.102 Angle : 0.379 5.798 45144 Z= 0.211 Chirality : 0.036 0.120 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.426 12.112 4320 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.72 % Allowed : 11.37 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.13), residues: 3984 helix: 2.87 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -0.80 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 110 TYR 0.016 0.001 TYR M 24 PHE 0.008 0.001 PHE X 129 TRP 0.001 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.10 (33408) covalent geometry : angle 0.37872 / 0.21 (45144) hydrogen bonds : bond 0.05256 / 3.53 ( 2550) hydrogen bonds : angle 3.48788 / 2.52 ( 7626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 371 time to evaluate : 1.396 Fit side-chains REVERT: A 60 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 107 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8415 (t0) REVERT: B 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8446 (t0) REVERT: C 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8399 (t0) REVERT: D 60 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: D 107 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8401 (t0) REVERT: E 60 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: E 107 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8421 (t0) REVERT: F 60 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: F 107 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8401 (t0) REVERT: G 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: H 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8472 (t0) REVERT: I 60 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: I 107 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8425 (t0) REVERT: J 107 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8387 (t0) REVERT: K 107 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8406 (t0) REVERT: L 60 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: L 107 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (t0) REVERT: M 60 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: M 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8422 (t0) REVERT: N 60 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: N 107 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8407 (t0) REVERT: O 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8420 (t0) REVERT: P 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8443 (t0) REVERT: Q 60 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: Q 107 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8412 (t0) REVERT: R 60 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7115 (m-30) REVERT: R 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (t0) REVERT: S 60 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: S 107 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (t0) REVERT: T 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8455 (t0) REVERT: U 60 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: U 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8403 (t0) REVERT: V 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8460 (t0) REVERT: W 60 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: W 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8420 (t0) REVERT: X 107 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (t0) outliers start: 37 outliers final: 0 residues processed: 406 average time/residue: 0.4393 time to fit residues: 230.9844 Evaluate side-chains 358 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 317 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 344 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125133 restraints weight = 207722.190| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.48 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 33408 Z= 0.142 Angle : 0.435 6.045 45144 Z= 0.242 Chirality : 0.037 0.128 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.550 12.863 4320 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.75 % Allowed : 13.37 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.13), residues: 3984 helix: 2.60 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.63 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 105 TYR 0.016 0.002 TYR V 24 PHE 0.010 0.001 PHE N 129 TRP 0.002 0.001 TRP A 180 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (33408) covalent geometry : angle 0.43506 / 0.24 (45144) hydrogen bonds : bond 0.07268 / 4.87 ( 2550) hydrogen bonds : angle 3.69076 / 2.67 ( 7626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 1.234 Fit side-chains REVERT: A 60 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: A 107 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8463 (t0) REVERT: B 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8453 (t0) REVERT: D 60 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: D 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8443 (t0) REVERT: E 60 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: E 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8434 (t0) REVERT: F 60 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: F 107 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (t0) REVERT: G 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8446 (t0) REVERT: H 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8463 (t0) REVERT: I 60 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: I 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8468 (t0) REVERT: J 107 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8489 (t0) REVERT: K 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8446 (t0) REVERT: L 60 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: L 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: M 60 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: M 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8466 (t0) REVERT: N 60 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: N 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: O 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8437 (t0) REVERT: P 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8459 (t0) REVERT: Q 60 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: Q 107 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8471 (t0) REVERT: R 60 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: R 107 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8447 (t0) REVERT: S 60 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: S 107 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8439 (t0) REVERT: T 107 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8471 (t0) REVERT: U 60 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: U 107 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8437 (t0) REVERT: V 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8455 (t0) REVERT: W 60 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: W 107 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8458 (t0) REVERT: X 107 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (t0) outliers start: 38 outliers final: 0 residues processed: 388 average time/residue: 0.4028 time to fit residues: 208.7168 Evaluate side-chains 380 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 18 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 360 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124364 restraints weight = 204203.462| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.44 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33408 Z= 0.142 Angle : 0.436 5.958 45144 Z= 0.242 Chirality : 0.037 0.122 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.591 12.997 4320 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.83 % Allowed : 13.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.70 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 105 TYR 0.015 0.002 TYR D 24 PHE 0.010 0.001 PHE I 129 TRP 0.001 0.001 TRP B 180 HIS 0.004 0.001 HIS R 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (33408) covalent geometry : angle 0.43559 / 0.24 (45144) hydrogen bonds : bond 0.07434 / 4.99 ( 2550) hydrogen bonds : angle 3.73349 / 2.70 ( 7626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 1.339 Fit side-chains REVERT: A 60 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: A 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8492 (t0) REVERT: B 107 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8469 (t0) REVERT: C 107 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8453 (t0) REVERT: D 60 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: D 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8458 (t0) REVERT: E 60 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: E 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8457 (t0) REVERT: F 60 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: F 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8438 (t0) REVERT: G 107 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8458 (t0) REVERT: H 107 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8474 (t0) REVERT: I 60 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: I 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8491 (t0) REVERT: J 107 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8454 (t0) REVERT: K 107 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8449 (t0) REVERT: L 60 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: L 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8457 (t0) REVERT: M 60 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: M 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8471 (t0) REVERT: N 60 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: N 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8455 (t0) REVERT: O 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8449 (t0) REVERT: P 107 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8462 (t0) REVERT: Q 60 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: Q 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8496 (t0) REVERT: R 60 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: R 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8433 (t0) REVERT: S 60 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: S 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8467 (t0) REVERT: T 107 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8480 (t0) REVERT: U 60 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: U 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8441 (t0) REVERT: V 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8468 (t0) REVERT: W 60 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: W 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8473 (t0) REVERT: X 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (t0) outliers start: 41 outliers final: 3 residues processed: 380 average time/residue: 0.4126 time to fit residues: 208.9962 Evaluate side-chains 385 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 345 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 261 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 274 optimal weight: 0.8980 chunk 376 optimal weight: 7.9990 chunk 334 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129218 restraints weight = 185103.316| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.11 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33408 Z= 0.119 Angle : 0.404 5.895 45144 Z= 0.225 Chirality : 0.036 0.116 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.497 12.859 4320 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.91 % Allowed : 13.23 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.13), residues: 3984 helix: 2.65 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.60 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 105 TYR 0.015 0.001 TYR D 24 PHE 0.010 0.001 PHE F 129 TRP 0.001 0.000 TRP K 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (33408) covalent geometry : angle 0.40413 / 0.23 (45144) hydrogen bonds : bond 0.06279 / 4.22 ( 2550) hydrogen bonds : angle 3.61483 / 2.61 ( 7626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 1.341 Fit side-chains REVERT: A 60 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: A 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8507 (t0) REVERT: B 107 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8507 (t0) REVERT: C 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8487 (t0) REVERT: D 60 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: D 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8491 (t0) REVERT: E 60 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: E 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8501 (t0) REVERT: F 60 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: F 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8469 (t0) REVERT: G 107 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8506 (t0) REVERT: H 107 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8506 (t0) REVERT: I 60 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: I 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8503 (t0) REVERT: J 107 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (t0) REVERT: K 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8487 (t0) REVERT: L 60 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: L 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: M 60 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: M 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8502 (t0) REVERT: N 60 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: N 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8482 (t0) REVERT: O 107 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (t0) REVERT: P 107 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8511 (t0) REVERT: Q 60 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: Q 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8496 (t0) REVERT: R 60 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: R 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (t0) REVERT: S 60 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: S 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8490 (t0) REVERT: T 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (t0) REVERT: U 60 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: U 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8468 (t0) REVERT: V 107 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8506 (t0) REVERT: W 60 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: W 107 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (t0) REVERT: X 107 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8493 (t0) outliers start: 44 outliers final: 0 residues processed: 356 average time/residue: 0.4149 time to fit residues: 196.6701 Evaluate side-chains 357 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 173 optimal weight: 20.0000 chunk 246 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 chunk 350 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130249 restraints weight = 193464.572| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.28 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.116 Angle : 0.399 5.962 45144 Z= 0.222 Chirality : 0.036 0.125 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.459 12.734 4320 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.72 % Allowed : 13.43 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.13), residues: 3984 helix: 2.71 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.54 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 105 TYR 0.014 0.001 TYR N 24 PHE 0.008 0.001 PHE I 129 TRP 0.001 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.12 (33408) covalent geometry : angle 0.39868 / 0.22 (45144) hydrogen bonds : bond 0.06078 / 4.08 ( 2550) hydrogen bonds : angle 3.57486 / 2.59 ( 7626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7284.24 seconds wall clock time: 126 minutes 0.25 seconds (7560.25 seconds total)