Starting phenix.real_space_refine on Mon Jul 6 03:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqx_37757/07_2026/8wqx_37757.cif" } resolution = 3.2 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= 0.002 sd= 0.082 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 20922 2.51 5 N 5325 2.21 5 O 6383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 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: 32726 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: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "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: 11.18, per 1000 atoms: 0.34 Number of scatterers: 32726 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 6383 8.00 N 5325 7.00 C 20922 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: 2.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7678 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 12 sheets defined 84.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 44 removed outlier: 3.915A 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: 4.581A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.600A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 44 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 123 removed outlier: 3.730A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.958A 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 removed outlier: 3.599A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 44 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 123 removed outlier: 3.726A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.691A pdb=" N ILE C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 44 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.654A pdb=" N ILE D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 44 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.726A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.703A pdb=" N ILE E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 44 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.687A pdb=" N ILE F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 44 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 4.623A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.600A pdb=" N ILE G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 44 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 4.625A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 44 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 3.521A pdb=" N PHE I 129 " --> pdb=" O ASP I 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 removed outlier: 3.650A pdb=" N ILE I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 44 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.600A pdb=" N ILE J 162 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 44 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 removed outlier: 3.602A pdb=" N ILE K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 44 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.724A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 3.518A pdb=" N PHE L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 removed outlier: 3.635A pdb=" N ILE L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 44 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 151 removed outlier: 3.522A pdb=" N PHE M 129 " --> pdb=" O ASP M 125 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP M 134 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 removed outlier: 3.615A pdb=" N ILE M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 44 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.615A pdb=" N ILE N 162 " --> pdb=" O ASP N 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 44 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 removed outlier: 3.688A pdb=" N ILE O 162 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 44 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.600A pdb=" N ILE P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 44 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.957A 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 removed outlier: 3.691A pdb=" N ILE Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 44 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.725A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.655A pdb=" N ILE R 162 " --> pdb=" O ASP R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 44 Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.731A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.519A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.615A pdb=" N ILE S 162 " --> pdb=" O ASP S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 44 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.730A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.599A pdb=" N ILE T 162 " --> pdb=" O ASP T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 44 Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 removed outlier: 3.612A pdb=" N ILE U 162 " --> pdb=" O ASP U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 44 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.603A pdb=" N ILE V 162 " --> pdb=" O ASP V 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 44 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 123 removed outlier: 3.715A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 3.522A pdb=" N PHE W 129 " --> pdb=" O ASP W 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.616A pdb=" N ILE W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 44 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.959A 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 removed outlier: 3.659A pdb=" N ILE X 162 " --> pdb=" O ASP X 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2611 hydrogen bonds defined for protein. 7785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10748 1.34 - 1.46: 4461 1.46 - 1.57: 18044 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33397 Sorted by residual: bond pdb=" C VAL K 28 " pdb=" O VAL K 28 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.69e-01 bond pdb=" C VAL J 28 " pdb=" O VAL J 28 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.69e-01 bond pdb=" C VAL C 28 " pdb=" O VAL C 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 bond pdb=" C VAL H 28 " pdb=" O VAL H 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 bond pdb=" C VAL I 28 " pdb=" O VAL I 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 ... (remaining 33392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 40328 0.78 - 1.56: 3968 1.56 - 2.33: 534 2.33 - 3.11: 227 3.11 - 3.89: 72 Bond angle restraints: 45129 Sorted by residual: angle pdb=" N ILE K 179 " pdb=" CA ILE K 179 " pdb=" C ILE K 179 " ideal model delta sigma weight residual 110.42 108.51 1.91 9.40e-01 1.13e+00 4.13e+00 angle pdb=" C VAL F 149 " pdb=" N VAL F 150 " pdb=" CA VAL F 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.98e+00 angle pdb=" C VAL W 149 " pdb=" N VAL W 150 " pdb=" CA VAL W 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.96e+00 angle pdb=" C VAL A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.96e+00 angle pdb=" C VAL I 149 " pdb=" N VAL I 150 " pdb=" CA VAL I 150 " ideal model delta sigma weight residual 120.64 117.79 2.85 1.66e+00 3.63e-01 2.95e+00 ... (remaining 45124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 17374 14.96 - 29.92: 1861 29.92 - 44.88: 566 44.88 - 59.84: 186 59.84 - 74.80: 48 Dihedral angle restraints: 20035 sinusoidal: 8134 harmonic: 11901 Sorted by residual: dihedral pdb=" CA ASP P 71 " pdb=" CB ASP P 71 " pdb=" CG ASP P 71 " pdb=" OD1 ASP P 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.96 54.96 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP Q 71 " pdb=" CB ASP Q 71 " pdb=" CG ASP Q 71 " pdb=" OD1 ASP Q 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.94 54.94 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP U 71 " pdb=" CB ASP U 71 " pdb=" CG ASP U 71 " pdb=" OD1 ASP U 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.91 54.91 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 20032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2315 0.025 - 0.049: 1539 0.049 - 0.074: 704 0.074 - 0.099: 234 0.099 - 0.123: 103 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CB VAL N 136 " pdb=" CA VAL N 136 " pdb=" CG1 VAL N 136 " pdb=" CG2 VAL N 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CB VAL Q 136 " pdb=" CA VAL Q 136 " pdb=" CG1 VAL Q 136 " pdb=" CG2 VAL Q 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 4892 not shown) Planarity restraints: 5806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 91 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO T 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO T 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO T 92 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 91 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO I 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO I 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 92 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE W 91 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO W 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO W 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO W 92 " -0.017 5.00e-02 4.00e+02 ... (remaining 5803 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 161 2.59 - 3.17: 26587 3.17 - 3.74: 48316 3.74 - 4.32: 66401 4.32 - 4.90: 112581 Nonbonded interactions: 254046 Sorted by model distance: nonbonded pdb=" NE2 HIS E 65 " pdb="FE FE E 201 " model vdw 2.012 3.080 nonbonded pdb=" NE2 HIS O 65 " pdb="FE FE O 201 " model vdw 2.012 3.080 nonbonded pdb=" NE2 HIS W 65 " pdb="FE FE W 201 " model vdw 2.012 3.080 nonbonded pdb=" NE2 HIS S 65 " pdb="FE FE S 201 " model vdw 2.012 3.080 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.012 3.080 ... (remaining 254041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 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 \ 171 or resid 178 through 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 33.450 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.005 0.023 33397 Z= 0.223 Angle : 0.515 3.888 45129 Z= 0.300 Chirality : 0.040 0.123 4895 Planarity : 0.003 0.030 5806 Dihedral : 14.735 74.802 12357 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 3.80 % Favored : 95.52 % 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: -1.24 (0.12), residues: 3983 helix: -0.08 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -3.17 (0.17), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 75 TYR 0.015 0.002 TYR U 126 PHE 0.006 0.001 PHE B 129 TRP 0.007 0.001 TRP B 134 HIS 0.003 0.001 HIS Q 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (33397) covalent geometry : angle 0.51481 / 0.30 (45129) hydrogen bonds : bond 0.13371 / 9.23 ( 2611) hydrogen bonds : angle 4.38140 / 3.13 ( 7785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7972 (mtt) cc_final: 0.7638 (mtt) REVERT: B 78 MET cc_start: 0.8036 (mtt) cc_final: 0.7700 (mtt) REVERT: D 78 MET cc_start: 0.8044 (mtt) cc_final: 0.7659 (mtt) REVERT: E 78 MET cc_start: 0.7960 (mtt) cc_final: 0.7624 (mtt) REVERT: F 78 MET cc_start: 0.8035 (mtt) cc_final: 0.7676 (mtt) REVERT: G 78 MET cc_start: 0.8011 (mtt) cc_final: 0.7660 (mtt) REVERT: H 78 MET cc_start: 0.7995 (mtt) cc_final: 0.7627 (mtt) REVERT: I 78 MET cc_start: 0.7950 (mtt) cc_final: 0.7624 (mtt) REVERT: J 78 MET cc_start: 0.7983 (mtt) cc_final: 0.7647 (mtt) REVERT: K 78 MET cc_start: 0.8007 (mtt) cc_final: 0.7669 (mtt) REVERT: L 78 MET cc_start: 0.8019 (mtt) cc_final: 0.7648 (mtt) REVERT: M 78 MET cc_start: 0.8036 (mtt) cc_final: 0.7673 (mtt) REVERT: N 78 MET cc_start: 0.8067 (mtt) cc_final: 0.7684 (mtt) REVERT: O 78 MET cc_start: 0.8021 (mtt) cc_final: 0.7673 (mtt) REVERT: P 78 MET cc_start: 0.8022 (mtt) cc_final: 0.7662 (mtt) REVERT: Q 78 MET cc_start: 0.7986 (mtt) cc_final: 0.7645 (mtt) REVERT: R 78 MET cc_start: 0.8050 (mtt) cc_final: 0.7652 (mtt) REVERT: S 78 MET cc_start: 0.8016 (mtt) cc_final: 0.7663 (mtt) REVERT: T 78 MET cc_start: 0.7962 (mtt) cc_final: 0.7619 (mtt) REVERT: U 78 MET cc_start: 0.8034 (mtt) cc_final: 0.7697 (mtt) REVERT: V 78 MET cc_start: 0.7987 (mtt) cc_final: 0.7652 (mtt) REVERT: W 78 MET cc_start: 0.8076 (mtt) cc_final: 0.7729 (mtt) REVERT: X 78 MET cc_start: 0.8056 (mtt) cc_final: 0.7701 (mtt) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1946 time to fit residues: 144.5933 Evaluate side-chains 255 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS B 23 HIS C 23 HIS D 23 HIS E 23 HIS F 23 HIS G 23 HIS H 23 HIS I 23 HIS J 23 HIS K 23 HIS L 23 HIS M 23 HIS N 23 HIS O 23 HIS P 23 HIS Q 23 HIS R 23 HIS S 23 HIS T 23 HIS U 23 HIS V 23 HIS W 23 HIS X 23 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113002 restraints weight = 339099.919| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 5.62 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33397 Z= 0.129 Angle : 0.455 4.649 45129 Z= 0.251 Chirality : 0.039 0.157 4895 Planarity : 0.003 0.033 5806 Dihedral : 3.586 11.564 4319 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.13 % Allowed : 8.93 % Favored : 89.95 % 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: 0.69 (0.13), residues: 3983 helix: 1.26 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.68 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 105 TYR 0.011 0.001 TYR J 24 PHE 0.007 0.001 PHE L 129 TRP 0.003 0.001 TRP T 134 HIS 0.003 0.001 HIS U 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (33397) covalent geometry : angle 0.45487 / 0.25 (45129) hydrogen bonds : bond 0.05918 / 3.96 ( 2611) hydrogen bonds : angle 3.19802 / 2.28 ( 7785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 374 time to evaluate : 0.868 Fit side-chains REVERT: A 78 MET cc_start: 0.8421 (mtt) cc_final: 0.8124 (mtt) REVERT: B 78 MET cc_start: 0.8449 (mtt) cc_final: 0.8159 (mtt) REVERT: C 78 MET cc_start: 0.8396 (mtt) cc_final: 0.8094 (mtt) REVERT: D 78 MET cc_start: 0.8448 (mtt) cc_final: 0.8156 (mtt) REVERT: E 78 MET cc_start: 0.8394 (mtt) cc_final: 0.8109 (mtt) REVERT: F 78 MET cc_start: 0.8423 (mtt) cc_final: 0.8140 (mtt) REVERT: G 78 MET cc_start: 0.8414 (mtt) cc_final: 0.8121 (mtt) REVERT: H 78 MET cc_start: 0.8432 (mtt) cc_final: 0.8155 (mtt) REVERT: I 78 MET cc_start: 0.8445 (mtt) cc_final: 0.8153 (mtt) REVERT: J 78 MET cc_start: 0.8433 (mtt) cc_final: 0.8145 (mtt) REVERT: K 78 MET cc_start: 0.8394 (mtt) cc_final: 0.8118 (mtt) REVERT: L 78 MET cc_start: 0.8429 (mtt) cc_final: 0.8142 (mtt) REVERT: M 78 MET cc_start: 0.8448 (mtt) cc_final: 0.8167 (mtt) REVERT: N 78 MET cc_start: 0.8463 (mtt) cc_final: 0.8179 (mtt) REVERT: O 78 MET cc_start: 0.8442 (mtt) cc_final: 0.8147 (mtt) REVERT: P 78 MET cc_start: 0.8422 (mtt) cc_final: 0.8128 (mtt) REVERT: Q 78 MET cc_start: 0.8447 (mtt) cc_final: 0.8168 (mtt) REVERT: R 78 MET cc_start: 0.8414 (mtt) cc_final: 0.8129 (mtt) REVERT: S 78 MET cc_start: 0.8451 (mtt) cc_final: 0.8159 (mtt) REVERT: T 78 MET cc_start: 0.8439 (mtt) cc_final: 0.8159 (mtt) REVERT: U 78 MET cc_start: 0.8424 (mtt) cc_final: 0.8144 (mtt) REVERT: V 78 MET cc_start: 0.8439 (mtt) cc_final: 0.8149 (mtt) REVERT: W 78 MET cc_start: 0.8441 (mtt) cc_final: 0.8152 (mtt) REVERT: W 148 ASP cc_start: 0.8579 (m-30) cc_final: 0.8379 (m-30) REVERT: X 78 MET cc_start: 0.8446 (mtt) cc_final: 0.8151 (mtt) outliers start: 16 outliers final: 0 residues processed: 377 average time/residue: 0.1523 time to fit residues: 101.6033 Evaluate side-chains 308 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 116 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 chunk 278 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 355 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 76 ASN B 17 ASN B 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 17 ASN H 76 ASN I 76 ASN J 17 ASN J 76 ASN K 76 ASN L 17 ASN L 76 ASN M 17 ASN M 76 ASN N 76 ASN O 17 ASN O 76 ASN P 17 ASN P 76 ASN Q 17 ASN Q 76 ASN R 17 ASN R 76 ASN S 17 ASN S 76 ASN T 76 ASN U 17 ASN U 76 ASN V 17 ASN V 76 ASN W 17 ASN W 76 ASN X 17 ASN X 76 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113847 restraints weight = 347323.784| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 5.86 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33397 Z= 0.117 Angle : 0.428 6.994 45129 Z= 0.238 Chirality : 0.036 0.119 4895 Planarity : 0.003 0.031 5806 Dihedral : 3.397 10.253 4319 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.46 % Allowed : 9.24 % Favored : 89.30 % 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: 1.57 (0.13), residues: 3983 helix: 1.94 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 105 TYR 0.010 0.001 TYR N 24 PHE 0.006 0.001 PHE W 129 TRP 0.003 0.001 TRP H 134 HIS 0.003 0.000 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (33397) covalent geometry : angle 0.42751 / 0.24 (45129) hydrogen bonds : bond 0.05323 / 3.57 ( 2611) hydrogen bonds : angle 3.03386 / 2.17 ( 7785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 335 time to evaluate : 1.299 Fit side-chains REVERT: W 148 ASP cc_start: 0.8459 (m-30) cc_final: 0.8228 (m-30) outliers start: 28 outliers final: 22 residues processed: 363 average time/residue: 0.1543 time to fit residues: 99.9394 Evaluate side-chains 310 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 12 optimal weight: 2.9990 chunk 372 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 319 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN F 76 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 76 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Q 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110779 restraints weight = 320370.744| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 5.57 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33397 Z= 0.139 Angle : 0.440 6.097 45129 Z= 0.246 Chirality : 0.037 0.108 4895 Planarity : 0.003 0.028 5806 Dihedral : 3.394 10.539 4319 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.21 % Allowed : 9.60 % Favored : 89.19 % 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: 1.82 (0.13), residues: 3983 helix: 2.09 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.39 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 105 TYR 0.013 0.001 TYR Q 24 PHE 0.006 0.001 PHE M 129 TRP 0.005 0.001 TRP D 134 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (33397) covalent geometry : angle 0.44035 / 0.25 (45129) hydrogen bonds : bond 0.06136 / 4.11 ( 2611) hydrogen bonds : angle 3.13516 / 2.24 ( 7785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 1.883 Fit side-chains REVERT: K 78 MET cc_start: 0.8380 (mtt) cc_final: 0.8179 (mtt) REVERT: U 78 MET cc_start: 0.8378 (mtt) cc_final: 0.8166 (mtt) REVERT: W 148 ASP cc_start: 0.8500 (m-30) cc_final: 0.8272 (m-30) outliers start: 19 outliers final: 0 residues processed: 328 average time/residue: 0.1565 time to fit residues: 91.3407 Evaluate side-chains 305 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 296 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 ASN D 76 ASN G 76 ASN H 76 ASN I 76 ASN L 17 ASN L 76 ASN N 76 ASN O 76 ASN U 17 ASN X 17 ASN X 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.104602 restraints weight = 338363.001| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 5.69 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 33397 Z= 0.208 Angle : 0.518 5.769 45129 Z= 0.286 Chirality : 0.041 0.128 4895 Planarity : 0.003 0.029 5806 Dihedral : 3.668 11.296 4319 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.41 % Allowed : 10.34 % Favored : 88.26 % 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: 1.58 (0.13), residues: 3983 helix: 1.89 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 105 TYR 0.015 0.002 TYR E 24 PHE 0.006 0.001 PHE M 129 TRP 0.008 0.001 TRP T 134 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (33397) covalent geometry : angle 0.51848 / 0.29 (45129) hydrogen bonds : bond 0.08270 / 5.52 ( 2611) hydrogen bonds : angle 3.55920 / 2.54 ( 7785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 1.284 Fit side-chains REVERT: C 78 MET cc_start: 0.8537 (mtt) cc_final: 0.8276 (mtt) outliers start: 26 outliers final: 20 residues processed: 330 average time/residue: 0.1921 time to fit residues: 103.4404 Evaluate side-chains 254 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain W residue 91 ILE Chi-restraints excluded: chain X residue 91 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 334 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 339 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.127446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109167 restraints weight = 331278.637| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 5.65 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33397 Z= 0.144 Angle : 0.445 5.355 45129 Z= 0.249 Chirality : 0.037 0.113 4895 Planarity : 0.003 0.029 5806 Dihedral : 3.533 10.897 4319 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.68 % Allowed : 11.74 % Favored : 87.58 % 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: 2.02 (0.13), residues: 3983 helix: 2.21 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.21 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 105 TYR 0.012 0.001 TYR H 24 PHE 0.006 0.001 PHE L 129 TRP 0.005 0.001 TRP I 134 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (33397) covalent geometry : angle 0.44530 / 0.25 (45129) hydrogen bonds : bond 0.06626 / 4.43 ( 2611) hydrogen bonds : angle 3.23034 / 2.31 ( 7785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.868 Fit side-chains REVERT: C 47 MET cc_start: 0.8420 (mmt) cc_final: 0.7553 (mmt) REVERT: D 47 MET cc_start: 0.8433 (mmt) cc_final: 0.7562 (mmt) REVERT: E 47 MET cc_start: 0.8440 (mmt) cc_final: 0.7569 (mmt) REVERT: F 47 MET cc_start: 0.8437 (mmt) cc_final: 0.7570 (mmt) REVERT: G 47 MET cc_start: 0.8565 (mmm) cc_final: 0.7704 (mmt) REVERT: I 47 MET cc_start: 0.8429 (mmt) cc_final: 0.7569 (mmt) REVERT: L 47 MET cc_start: 0.8561 (mmm) cc_final: 0.7694 (mmt) REVERT: M 47 MET cc_start: 0.8555 (mmm) cc_final: 0.7687 (mmt) REVERT: N 47 MET cc_start: 0.8564 (mmm) cc_final: 0.7709 (mmt) REVERT: P 47 MET cc_start: 0.8560 (mmm) cc_final: 0.7714 (mmt) REVERT: Q 47 MET cc_start: 0.8449 (mmt) cc_final: 0.7575 (mmt) REVERT: R 47 MET cc_start: 0.8446 (mmt) cc_final: 0.7577 (mmt) REVERT: U 47 MET cc_start: 0.8564 (mmm) cc_final: 0.7701 (mmt) REVERT: V 47 MET cc_start: 0.8552 (mmm) cc_final: 0.7701 (mmt) REVERT: W 47 MET cc_start: 0.8586 (mmm) cc_final: 0.7731 (mmt) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1544 time to fit residues: 77.6642 Evaluate side-chains 273 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 357 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 327 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 328 optimal weight: 0.8980 chunk 376 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 GLN D 17 ASN E 17 ASN G 17 ASN I 17 ASN K 17 ASN L 17 ASN N 17 ASN T 17 ASN U 17 ASN X 17 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115750 restraints weight = 304802.383| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 5.61 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33397 Z= 0.107 Angle : 0.392 5.079 45129 Z= 0.220 Chirality : 0.036 0.109 4895 Planarity : 0.003 0.028 5806 Dihedral : 3.350 10.102 4319 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.68 % Allowed : 12.25 % Favored : 87.07 % 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: 2.65 (0.13), residues: 3983 helix: 2.66 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 105 TYR 0.009 0.001 TYR E 24 PHE 0.006 0.001 PHE L 129 TRP 0.003 0.001 TRP P 134 HIS 0.003 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.11 (33397) covalent geometry : angle 0.39163 / 0.22 (45129) hydrogen bonds : bond 0.04962 / 3.33 ( 2611) hydrogen bonds : angle 2.90442 / 2.08 ( 7785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.193 Fit side-chains REVERT: A 47 MET cc_start: 0.8118 (mmt) cc_final: 0.7433 (mmt) REVERT: B 47 MET cc_start: 0.8139 (mmt) cc_final: 0.7439 (mmt) REVERT: C 47 MET cc_start: 0.8300 (mmt) cc_final: 0.7543 (mmt) REVERT: D 47 MET cc_start: 0.8345 (mmt) cc_final: 0.7565 (mmt) REVERT: E 47 MET cc_start: 0.8326 (mmt) cc_final: 0.7564 (mmt) REVERT: F 47 MET cc_start: 0.8322 (mmt) cc_final: 0.7562 (mmt) REVERT: H 47 MET cc_start: 0.8107 (mmt) cc_final: 0.7431 (mmt) REVERT: I 47 MET cc_start: 0.8335 (mmt) cc_final: 0.7563 (mmt) REVERT: I 125 ASP cc_start: 0.7968 (t0) cc_final: 0.7432 (t70) REVERT: J 47 MET cc_start: 0.8103 (mmt) cc_final: 0.7404 (mmt) REVERT: K 47 MET cc_start: 0.8124 (mmt) cc_final: 0.7431 (mmt) REVERT: O 47 MET cc_start: 0.8100 (mmt) cc_final: 0.7447 (mmt) REVERT: Q 47 MET cc_start: 0.8322 (mmt) cc_final: 0.7539 (mmt) REVERT: R 47 MET cc_start: 0.8355 (mmt) cc_final: 0.7583 (mmt) REVERT: S 47 MET cc_start: 0.8134 (mmt) cc_final: 0.7438 (mmt) REVERT: T 47 MET cc_start: 0.8115 (mmt) cc_final: 0.7412 (mmt) REVERT: W 125 ASP cc_start: 0.8013 (t0) cc_final: 0.7482 (t70) REVERT: X 47 MET cc_start: 0.8103 (mmt) cc_final: 0.7404 (mmt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1551 time to fit residues: 93.2272 Evaluate side-chains 313 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 22 optimal weight: 4.9990 chunk 370 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 327 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 L 22 GLN M 22 GLN N 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108424 restraints weight = 337558.528| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.76 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33397 Z= 0.157 Angle : 0.454 5.058 45129 Z= 0.253 Chirality : 0.038 0.113 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.474 10.526 4319 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.70 % Allowed : 12.39 % 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: 2.49 (0.13), residues: 3983 helix: 2.53 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 105 TYR 0.014 0.001 TYR Q 24 PHE 0.005 0.001 PHE L 129 TRP 0.006 0.001 TRP O 134 HIS 0.003 0.001 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (33397) covalent geometry : angle 0.45429 / 0.25 (45129) hydrogen bonds : bond 0.06881 / 4.60 ( 2611) hydrogen bonds : angle 3.26436 / 2.34 ( 7785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.186 Fit side-chains REVERT: A 47 MET cc_start: 0.8406 (mmt) cc_final: 0.7600 (mmt) REVERT: C 47 MET cc_start: 0.8562 (mmt) cc_final: 0.7738 (mmt) REVERT: C 78 MET cc_start: 0.8559 (mtt) cc_final: 0.8287 (mtt) REVERT: D 47 MET cc_start: 0.8564 (mmt) cc_final: 0.7726 (mmt) REVERT: E 47 MET cc_start: 0.8578 (mmt) cc_final: 0.7762 (mmt) REVERT: G 47 MET cc_start: 0.8545 (mmt) cc_final: 0.7653 (mmt) REVERT: H 47 MET cc_start: 0.8406 (mmt) cc_final: 0.7603 (mmt) REVERT: I 47 MET cc_start: 0.8569 (mmt) cc_final: 0.7751 (mmt) REVERT: L 47 MET cc_start: 0.8549 (mmt) cc_final: 0.7652 (mmt) REVERT: M 47 MET cc_start: 0.8555 (mmt) cc_final: 0.7664 (mmt) REVERT: N 47 MET cc_start: 0.8526 (mmt) cc_final: 0.7651 (mmt) REVERT: O 47 MET cc_start: 0.8443 (mmt) cc_final: 0.7618 (mmt) REVERT: P 47 MET cc_start: 0.8530 (mmt) cc_final: 0.7649 (mmt) REVERT: Q 47 MET cc_start: 0.8573 (mmt) cc_final: 0.7750 (mmt) REVERT: R 47 MET cc_start: 0.8574 (mmt) cc_final: 0.7745 (mmt) REVERT: U 47 MET cc_start: 0.8545 (mmt) cc_final: 0.7660 (mmt) REVERT: V 47 MET cc_start: 0.8532 (mmt) cc_final: 0.7642 (mmt) REVERT: W 47 MET cc_start: 0.8568 (mmt) cc_final: 0.7672 (mmt) REVERT: X 47 MET cc_start: 0.8405 (mmt) cc_final: 0.7566 (mmt) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1546 time to fit residues: 67.5580 Evaluate side-chains 247 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 210 optimal weight: 6.9990 chunk 348 optimal weight: 0.1980 chunk 187 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 333 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 198 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 76 ASN U 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113312 restraints weight = 308913.160| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 5.66 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33397 Z= 0.115 Angle : 0.402 4.873 45129 Z= 0.226 Chirality : 0.036 0.107 4895 Planarity : 0.003 0.024 5806 Dihedral : 3.381 10.005 4319 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 12.50 % Favored : 86.82 % 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: 2.80 (0.13), residues: 3983 helix: 2.75 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -2.07 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 105 TYR 0.011 0.001 TYR W 24 PHE 0.006 0.001 PHE L 129 TRP 0.004 0.001 TRP D 134 HIS 0.003 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (33397) covalent geometry : angle 0.40189 / 0.23 (45129) hydrogen bonds : bond 0.05463 / 3.66 ( 2611) hydrogen bonds : angle 3.00327 / 2.15 ( 7785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.143 Fit side-chains REVERT: A 47 MET cc_start: 0.8171 (mmt) cc_final: 0.7471 (mmt) REVERT: B 47 MET cc_start: 0.8166 (mmt) cc_final: 0.7444 (mmt) REVERT: C 47 MET cc_start: 0.8348 (mmt) cc_final: 0.7558 (mmt) REVERT: C 78 MET cc_start: 0.8424 (mtt) cc_final: 0.8117 (mtt) REVERT: D 47 MET cc_start: 0.8382 (mmt) cc_final: 0.7582 (mmt) REVERT: E 47 MET cc_start: 0.8369 (mmt) cc_final: 0.7588 (mmt) REVERT: F 47 MET cc_start: 0.8128 (mmt) cc_final: 0.7443 (mmt) REVERT: G 47 MET cc_start: 0.8360 (mmt) cc_final: 0.7582 (mmt) REVERT: H 47 MET cc_start: 0.8174 (mmt) cc_final: 0.7477 (mmt) REVERT: I 47 MET cc_start: 0.8354 (mmt) cc_final: 0.7567 (mmt) REVERT: J 47 MET cc_start: 0.8142 (mmt) cc_final: 0.7435 (mmt) REVERT: K 47 MET cc_start: 0.8176 (mmt) cc_final: 0.7471 (mmt) REVERT: L 47 MET cc_start: 0.8389 (mmt) cc_final: 0.7610 (mmt) REVERT: M 47 MET cc_start: 0.8379 (mmt) cc_final: 0.7592 (mmt) REVERT: N 47 MET cc_start: 0.8396 (mmt) cc_final: 0.7599 (mmt) REVERT: O 47 MET cc_start: 0.8172 (mmt) cc_final: 0.7460 (mmt) REVERT: P 47 MET cc_start: 0.8363 (mmt) cc_final: 0.7592 (mmt) REVERT: Q 47 MET cc_start: 0.8347 (mmt) cc_final: 0.7550 (mmt) REVERT: R 47 MET cc_start: 0.8371 (mmt) cc_final: 0.7584 (mmt) REVERT: S 47 MET cc_start: 0.8195 (mmt) cc_final: 0.7483 (mmt) REVERT: T 47 MET cc_start: 0.8157 (mmt) cc_final: 0.7437 (mmt) REVERT: U 47 MET cc_start: 0.8370 (mmt) cc_final: 0.7587 (mmt) REVERT: V 47 MET cc_start: 0.8376 (mmt) cc_final: 0.7583 (mmt) REVERT: W 47 MET cc_start: 0.8401 (mmt) cc_final: 0.7610 (mmt) REVERT: X 47 MET cc_start: 0.8131 (mmt) cc_final: 0.7435 (mmt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1474 time to fit residues: 75.7784 Evaluate side-chains 288 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 22 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN C 22 GLN E 22 GLN H 22 GLN K 22 GLN M 22 GLN N 22 GLN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN T 22 GLN U 22 GLN V 22 GLN X 22 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109560 restraints weight = 324399.613| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.84 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33397 Z= 0.152 Angle : 0.448 5.001 45129 Z= 0.249 Chirality : 0.038 0.111 4895 Planarity : 0.003 0.025 5806 Dihedral : 3.451 10.509 4319 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 12.50 % Favored : 86.82 % 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: 2.56 (0.13), residues: 3983 helix: 2.58 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.00 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 105 TYR 0.014 0.001 TYR I 24 PHE 0.005 0.001 PHE M 129 TRP 0.007 0.001 TRP D 134 HIS 0.003 0.001 HIS M 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (33397) covalent geometry : angle 0.44779 / 0.25 (45129) hydrogen bonds : bond 0.06723 / 4.49 ( 2611) hydrogen bonds : angle 3.23543 / 2.32 ( 7785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.308 Fit side-chains REVERT: A 47 MET cc_start: 0.8402 (mmt) cc_final: 0.7597 (mmt) REVERT: C 47 MET cc_start: 0.8577 (mmt) cc_final: 0.7751 (mmt) REVERT: C 78 MET cc_start: 0.8469 (mtt) cc_final: 0.8172 (mtt) REVERT: D 47 MET cc_start: 0.8571 (mmt) cc_final: 0.7734 (mmt) REVERT: E 47 MET cc_start: 0.8583 (mmt) cc_final: 0.7767 (mmt) REVERT: F 47 MET cc_start: 0.8426 (mmt) cc_final: 0.7683 (mmt) REVERT: G 47 MET cc_start: 0.8585 (mmt) cc_final: 0.7709 (mmt) REVERT: H 47 MET cc_start: 0.8419 (mmt) cc_final: 0.7622 (mmt) REVERT: I 47 MET cc_start: 0.8577 (mmt) cc_final: 0.7766 (mmt) REVERT: L 47 MET cc_start: 0.8595 (mmt) cc_final: 0.7718 (mmt) REVERT: M 47 MET cc_start: 0.8594 (mmt) cc_final: 0.7719 (mmt) REVERT: N 47 MET cc_start: 0.8559 (mmt) cc_final: 0.7689 (mmt) REVERT: O 47 MET cc_start: 0.8445 (mmt) cc_final: 0.7617 (mmt) REVERT: P 47 MET cc_start: 0.8561 (mmt) cc_final: 0.7701 (mmt) REVERT: Q 47 MET cc_start: 0.8582 (mmt) cc_final: 0.7755 (mmt) REVERT: R 47 MET cc_start: 0.8580 (mmt) cc_final: 0.7760 (mmt) REVERT: U 47 MET cc_start: 0.8576 (mmt) cc_final: 0.7704 (mmt) REVERT: V 47 MET cc_start: 0.8578 (mmt) cc_final: 0.7714 (mmt) REVERT: W 47 MET cc_start: 0.8603 (mmt) cc_final: 0.7723 (mmt) REVERT: X 47 MET cc_start: 0.8444 (mmt) cc_final: 0.7584 (mmt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1601 time to fit residues: 72.2564 Evaluate side-chains 255 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 121 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 207 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.130748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112361 restraints weight = 326253.420| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 5.74 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 33397 Z= 0.119 Angle : 0.405 4.768 45129 Z= 0.227 Chirality : 0.036 0.107 4895 Planarity : 0.003 0.024 5806 Dihedral : 3.388 9.972 4319 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 12.73 % Favored : 86.60 % 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: 2.76 (0.13), residues: 3983 helix: 2.73 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.93 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 105 TYR 0.011 0.001 TYR B 24 PHE 0.006 0.001 PHE W 129 TRP 0.003 0.001 TRP L 134 HIS 0.003 0.001 HIS R 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (33397) covalent geometry : angle 0.40461 / 0.23 (45129) hydrogen bonds : bond 0.05635 / 3.78 ( 2611) hydrogen bonds : angle 3.02198 / 2.16 ( 7785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.81 seconds wall clock time: 82 minutes 28.80 seconds (4948.80 seconds total)