Starting phenix.real_space_refine on Tue Aug 26 01:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqx_37757/08_2025/8wqx_37757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqx_37757/08_2025/8wqx_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_37757/08_2025/8wqx_37757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqx_37757/08_2025/8wqx_37757.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqx_37757/08_2025/8wqx_37757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqx_37757/08_2025/8wqx_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 11.85, per 1000 atoms: 0.36 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: 2.82 Conformation dependent library (CDL) restraints added in 2.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.88 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: 5.79 Time building geometry restraints manager: 3.83 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 2.340 nonbonded pdb=" NE2 HIS O 65 " pdb="FE FE O 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS W 65 " pdb="FE FE W 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS S 65 " pdb="FE FE S 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.012 2.340 ... (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: 1.020 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.220 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 aren 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 covalent geometry : bond 0.00502 (33397) covalent geometry : angle 0.51481 (45129) hydrogen bonds : bond 0.13371 ( 2611) hydrogen bonds : angle 4.38140 ( 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 : 1.017 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: 0.7659 (mtt) REVERT: H 78 MET cc_start: 0.7995 (mtt) cc_final: 0.7626 (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: 0.7672 (mtt) REVERT: N 78 MET cc_start: 0.8066 (mtt) cc_final: 0.7684 (mtt) REVERT: O 78 MET cc_start: 0.8021 (mtt) cc_final: 0.7672 (mtt) REVERT: P 78 MET cc_start: 0.8022 (mtt) cc_final: 0.7662 (mtt) REVERT: Q 78 MET cc_start: 0.7987 (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: 0.7664 (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: 0.8055 (mtt) cc_final: 0.7701 (mtt) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1957 time to fit residues: 145.3846 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 : 1.200 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 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: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3766 r_free = 0.3766 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110617 restraints weight = 340109.445| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 5.88 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33397 Z= 0.129 Angle : 0.455 4.786 45129 Z= 0.250 Chirality : 0.039 0.153 4895 Planarity : 0.003 0.032 5806 Dihedral : 3.581 11.451 4319 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.04 % Allowed : 9.04 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.13), residues: 3983 helix: 1.27 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.67 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 105 TYR 0.011 0.001 TYR J 24 PHE 0.007 0.001 PHE E 129 TRP 0.003 0.001 TRP R 180 HIS 0.003 0.001 HIS U 39 Details of bonding type rmsd covalent geometry : bond 0.00250 (33397) covalent geometry : angle 0.45536 (45129) hydrogen bonds : bond 0.05874 ( 2611) hydrogen bonds : angle 3.20059 ( 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 387 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 374 time to evaluate : 1.027 Fit side-chains REVERT: A 78 MET cc_start: 0.8396 (mtt) cc_final: 0.8106 (mtt) REVERT: B 78 MET cc_start: 0.8416 (mtt) cc_final: 0.8131 (mtt) REVERT: C 78 MET cc_start: 0.8383 (mtt) cc_final: 0.8084 (mtt) REVERT: D 148 ASP cc_start: 0.8674 (m-30) cc_final: 0.8467 (m-30) REVERT: E 78 MET cc_start: 0.8378 (mtt) cc_final: 0.8100 (mtt) REVERT: G 78 MET cc_start: 0.8403 (mtt) cc_final: 0.8114 (mtt) REVERT: H 78 MET cc_start: 0.8431 (mtt) cc_final: 0.8156 (mtt) REVERT: I 78 MET cc_start: 0.8417 (mtt) cc_final: 0.8134 (mtt) REVERT: J 78 MET cc_start: 0.8432 (mtt) cc_final: 0.8145 (mtt) REVERT: K 78 MET cc_start: 0.8394 (mtt) cc_final: 0.8124 (mtt) REVERT: M 78 MET cc_start: 0.8431 (mtt) cc_final: 0.8155 (mtt) REVERT: N 78 MET cc_start: 0.8436 (mtt) cc_final: 0.8162 (mtt) REVERT: O 78 MET cc_start: 0.8430 (mtt) cc_final: 0.8143 (mtt) REVERT: P 78 MET cc_start: 0.8404 (mtt) cc_final: 0.8114 (mtt) REVERT: R 78 MET cc_start: 0.8398 (mtt) cc_final: 0.8118 (mtt) REVERT: S 78 MET cc_start: 0.8429 (mtt) cc_final: 0.8142 (mtt) REVERT: T 78 MET cc_start: 0.8410 (mtt) cc_final: 0.8138 (mtt) REVERT: U 78 MET cc_start: 0.8412 (mtt) cc_final: 0.8143 (mtt) REVERT: V 78 MET cc_start: 0.8426 (mtt) cc_final: 0.8143 (mtt) REVERT: W 78 MET cc_start: 0.8428 (mtt) cc_final: 0.8144 (mtt) REVERT: X 78 MET cc_start: 0.8431 (mtt) cc_final: 0.8139 (mtt) outliers start: 13 outliers final: 0 residues processed: 374 average time/residue: 0.1537 time to fit residues: 102.0607 Evaluate side-chains 310 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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: 0.9980 chunk 278 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 363 optimal weight: 8.9990 chunk 313 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 76 ASN B 17 ASN B 76 ASN D 17 ASN D 76 ASN E 17 ASN E 76 ASN F 76 ASN G 17 ASN G 76 ASN H 17 ASN H 76 ASN I 17 ASN I 76 ASN J 17 ASN J 76 ASN K 17 ASN K 76 ASN L 76 ASN M 17 ASN M 76 ASN N 17 ASN N 76 ASN O 17 ASN O 76 ASN P 17 ASN P 76 ASN Q 76 ASN R 17 ASN R 76 ASN S 17 ASN S 76 ASN T 17 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116442 restraints weight = 348899.637| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 5.92 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33397 Z= 0.111 Angle : 0.418 7.224 45129 Z= 0.233 Chirality : 0.035 0.117 4895 Planarity : 0.003 0.030 5806 Dihedral : 3.388 10.081 4319 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.32 % Allowed : 9.60 % Favored : 89.07 % 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 aren not related in a simple way. whole: 1.65 (0.13), residues: 3983 helix: 2.00 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.57 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 105 TYR 0.010 0.001 TYR G 24 PHE 0.006 0.001 PHE W 129 TRP 0.003 0.001 TRP H 134 HIS 0.003 0.000 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00205 (33397) covalent geometry : angle 0.41785 (45129) hydrogen bonds : bond 0.05016 ( 2611) hydrogen bonds : angle 2.98886 ( 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 358 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 1.252 Fit side-chains REVERT: D 148 ASP cc_start: 0.8333 (m-30) cc_final: 0.8104 (m-30) outliers start: 23 outliers final: 21 residues processed: 358 average time/residue: 0.1532 time to fit residues: 97.4708 Evaluate side-chains 332 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 372 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 55 optimal weight: 0.0000 chunk 319 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN E 76 ASN F 17 ASN F 76 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN L 17 ASN L 76 ASN M 76 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN V 76 ASN ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117475 restraints weight = 312558.212| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 5.51 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 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 = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33397 Z= 0.110 Angle : 0.402 6.108 45129 Z= 0.226 Chirality : 0.035 0.110 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.309 11.379 4319 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.01 % Allowed : 10.56 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.13), residues: 3983 helix: 2.34 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.25 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 105 TYR 0.010 0.001 TYR G 24 PHE 0.006 0.001 PHE S 129 TRP 0.003 0.001 TRP H 134 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00202 (33397) covalent geometry : angle 0.40180 (45129) hydrogen bonds : bond 0.04916 ( 2611) hydrogen bonds : angle 2.92921 ( 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 339 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 1.148 Fit side-chains REVERT: D 148 ASP cc_start: 0.8334 (m-30) cc_final: 0.8083 (m-30) REVERT: G 78 MET cc_start: 0.8267 (mtt) cc_final: 0.8045 (mtt) REVERT: J 78 MET cc_start: 0.8287 (mtt) cc_final: 0.8066 (mtt) REVERT: P 78 MET cc_start: 0.8280 (mtt) cc_final: 0.8065 (mtt) REVERT: S 78 MET cc_start: 0.8307 (mtt) cc_final: 0.8095 (mtt) REVERT: T 78 MET cc_start: 0.8302 (mtt) cc_final: 0.8096 (mtt) REVERT: W 78 MET cc_start: 0.8311 (mtt) cc_final: 0.8103 (mtt) outliers start: 12 outliers final: 1 residues processed: 339 average time/residue: 0.1621 time to fit residues: 95.3429 Evaluate side-chains 313 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ASN 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: 3.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 350 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 76 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN O 76 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN W 22 GLN X 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108616 restraints weight = 342083.541| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 5.78 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33397 Z= 0.153 Angle : 0.455 5.721 45129 Z= 0.253 Chirality : 0.038 0.112 4895 Planarity : 0.003 0.025 5806 Dihedral : 3.456 12.105 4319 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.01 % Allowed : 10.79 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.13), residues: 3983 helix: 2.28 (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 0.004 0.001 ARG N 105 TYR 0.014 0.001 TYR D 24 PHE 0.006 0.001 PHE M 129 TRP 0.006 0.001 TRP B 134 HIS 0.003 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00324 (33397) covalent geometry : angle 0.45547 (45129) hydrogen bonds : bond 0.06767 ( 2611) hydrogen bonds : angle 3.24817 ( 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 329 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 317 time to evaluate : 1.064 Fit side-chains REVERT: A 47 MET cc_start: 0.8541 (mmt) cc_final: 0.7711 (mmt) REVERT: B 47 MET cc_start: 0.8572 (mmt) cc_final: 0.7714 (mmt) REVERT: C 47 MET cc_start: 0.8549 (mmt) cc_final: 0.7710 (mmt) REVERT: C 78 MET cc_start: 0.8484 (mtt) cc_final: 0.8185 (mtt) REVERT: D 47 MET cc_start: 0.8563 (mmt) cc_final: 0.7713 (mmt) REVERT: D 148 ASP cc_start: 0.8570 (m-30) cc_final: 0.8370 (m-30) REVERT: E 47 MET cc_start: 0.8554 (mmt) cc_final: 0.7707 (mmt) REVERT: F 47 MET cc_start: 0.8548 (mmt) cc_final: 0.7702 (mmt) REVERT: G 47 MET cc_start: 0.8570 (mmt) cc_final: 0.7690 (mmt) REVERT: G 78 MET cc_start: 0.8518 (mtt) cc_final: 0.8232 (mtt) REVERT: H 47 MET cc_start: 0.8584 (mmt) cc_final: 0.7753 (mmt) REVERT: I 47 MET cc_start: 0.8553 (mmt) cc_final: 0.7719 (mmt) REVERT: J 47 MET cc_start: 0.8544 (mmt) cc_final: 0.7676 (mmt) REVERT: J 78 MET cc_start: 0.8502 (mtt) cc_final: 0.8206 (mtt) REVERT: K 47 MET cc_start: 0.8547 (mmt) cc_final: 0.7676 (mmt) REVERT: L 47 MET cc_start: 0.8552 (mmt) cc_final: 0.7684 (mmt) REVERT: M 47 MET cc_start: 0.8576 (mmt) cc_final: 0.7713 (mmt) REVERT: N 47 MET cc_start: 0.8562 (mmt) cc_final: 0.7702 (mmt) REVERT: O 47 MET cc_start: 0.8563 (mmt) cc_final: 0.7701 (mmt) REVERT: P 78 MET cc_start: 0.8513 (mtt) cc_final: 0.8232 (mtt) REVERT: Q 47 MET cc_start: 0.8546 (mmt) cc_final: 0.7699 (mmt) REVERT: R 47 MET cc_start: 0.8567 (mmt) cc_final: 0.7710 (mmt) REVERT: S 47 MET cc_start: 0.8565 (mmt) cc_final: 0.7692 (mmt) REVERT: S 78 MET cc_start: 0.8524 (mtt) cc_final: 0.8254 (mtt) REVERT: T 47 MET cc_start: 0.8573 (mmt) cc_final: 0.7707 (mmt) REVERT: T 78 MET cc_start: 0.8518 (mtt) cc_final: 0.8246 (mtt) REVERT: U 47 MET cc_start: 0.8563 (mmt) cc_final: 0.7702 (mmt) REVERT: V 47 MET cc_start: 0.8554 (mmt) cc_final: 0.7700 (mmt) REVERT: W 47 MET cc_start: 0.8574 (mmt) cc_final: 0.7706 (mmt) REVERT: W 78 MET cc_start: 0.8518 (mtt) cc_final: 0.8262 (mtt) REVERT: X 47 MET cc_start: 0.8536 (mmt) cc_final: 0.7655 (mmt) outliers start: 12 outliers final: 0 residues processed: 329 average time/residue: 0.1727 time to fit residues: 98.5350 Evaluate side-chains 280 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 119 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 339 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113220 restraints weight = 333603.153| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 5.75 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33397 Z= 0.115 Angle : 0.400 5.297 45129 Z= 0.224 Chirality : 0.036 0.108 4895 Planarity : 0.003 0.027 5806 Dihedral : 3.373 13.589 4319 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.73 % Allowed : 12.73 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.13), residues: 3983 helix: 2.59 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.01 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 105 TYR 0.010 0.001 TYR H 24 PHE 0.006 0.001 PHE W 129 TRP 0.004 0.001 TRP I 134 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00216 (33397) covalent geometry : angle 0.40029 (45129) hydrogen bonds : bond 0.05366 ( 2611) hydrogen bonds : angle 2.97892 ( 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 335 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 1.289 Fit side-chains REVERT: A 47 MET cc_start: 0.8383 (mmt) cc_final: 0.7568 (mmt) REVERT: B 47 MET cc_start: 0.8500 (mmt) cc_final: 0.7710 (mmt) REVERT: C 47 MET cc_start: 0.8330 (mmt) cc_final: 0.7551 (mmt) REVERT: C 78 MET cc_start: 0.8436 (mtt) cc_final: 0.8139 (mtt) REVERT: D 47 MET cc_start: 0.8372 (mmt) cc_final: 0.7579 (mmt) REVERT: D 148 ASP cc_start: 0.8403 (m-30) cc_final: 0.8171 (m-30) REVERT: E 47 MET cc_start: 0.8359 (mmt) cc_final: 0.7597 (mmt) REVERT: F 47 MET cc_start: 0.8344 (mmt) cc_final: 0.7568 (mmt) REVERT: G 78 MET cc_start: 0.8446 (mtt) cc_final: 0.8143 (mtt) REVERT: H 47 MET cc_start: 0.8405 (mmt) cc_final: 0.7599 (mmt) REVERT: I 47 MET cc_start: 0.8342 (mmt) cc_final: 0.7560 (mmt) REVERT: J 78 MET cc_start: 0.8435 (mtt) cc_final: 0.8137 (mtt) REVERT: M 47 MET cc_start: 0.8406 (mmt) cc_final: 0.7604 (mmt) REVERT: O 47 MET cc_start: 0.8450 (mmt) cc_final: 0.7683 (mmt) REVERT: P 47 MET cc_start: 0.8365 (mmt) cc_final: 0.7572 (mmt) REVERT: P 78 MET cc_start: 0.8450 (mtt) cc_final: 0.8148 (mtt) REVERT: Q 47 MET cc_start: 0.8347 (mmt) cc_final: 0.7561 (mmt) REVERT: R 47 MET cc_start: 0.8390 (mmt) cc_final: 0.7597 (mmt) REVERT: S 78 MET cc_start: 0.8464 (mtt) cc_final: 0.8177 (mtt) REVERT: T 47 MET cc_start: 0.8477 (mmt) cc_final: 0.7678 (mmt) REVERT: T 78 MET cc_start: 0.8459 (mtt) cc_final: 0.8174 (mtt) REVERT: V 47 MET cc_start: 0.8486 (mmt) cc_final: 0.7710 (mmt) REVERT: W 47 MET cc_start: 0.8419 (mmt) cc_final: 0.7612 (mmt) REVERT: W 78 MET cc_start: 0.8453 (mtt) cc_final: 0.8168 (mtt) REVERT: X 47 MET cc_start: 0.8452 (mmt) cc_final: 0.7672 (mmt) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.1815 time to fit residues: 102.3098 Evaluate side-chains 312 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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: 9.9990 chunk 111 optimal weight: 4.9990 chunk 379 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN D 76 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106204 restraints weight = 313933.011| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 5.56 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 33397 Z= 0.183 Angle : 0.487 5.157 45129 Z= 0.271 Chirality : 0.040 0.122 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.570 12.393 4319 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.73 % Allowed : 13.69 % Favored : 85.58 % 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 aren not related in a simple way. whole: 2.25 (0.13), residues: 3983 helix: 2.36 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -2.22 (0.17), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 105 TYR 0.015 0.002 TYR N 24 PHE 0.005 0.001 PHE L 129 TRP 0.008 0.001 TRP L 134 HIS 0.003 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00406 (33397) covalent geometry : angle 0.48738 (45129) hydrogen bonds : bond 0.07600 ( 2611) hydrogen bonds : angle 3.42281 ( 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 261 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 1.320 Fit side-chains REVERT: A 47 MET cc_start: 0.8572 (mmt) cc_final: 0.7654 (mmt) REVERT: C 78 MET cc_start: 0.8542 (mtt) cc_final: 0.8265 (mtt) REVERT: G 78 MET cc_start: 0.8562 (mtt) cc_final: 0.8285 (mtt) REVERT: J 78 MET cc_start: 0.8557 (mtt) cc_final: 0.8279 (mtt) REVERT: P 78 MET cc_start: 0.8572 (mtt) cc_final: 0.8289 (mtt) REVERT: R 47 MET cc_start: 0.8580 (mmt) cc_final: 0.7668 (mmt) REVERT: S 78 MET cc_start: 0.8584 (mtt) cc_final: 0.8317 (mtt) REVERT: T 78 MET cc_start: 0.8561 (mtt) cc_final: 0.8292 (mtt) REVERT: W 78 MET cc_start: 0.8578 (mtt) cc_final: 0.8310 (mtt) outliers start: 2 outliers final: 1 residues processed: 261 average time/residue: 0.1635 time to fit residues: 74.8166 Evaluate side-chains 244 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 22 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107082 restraints weight = 347398.919| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 5.78 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33397 Z= 0.163 Angle : 0.467 5.518 45129 Z= 0.260 Chirality : 0.039 0.112 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.569 12.608 4319 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.76 % Allowed : 13.52 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.13), residues: 3983 helix: 2.38 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -2.20 (0.17), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 105 TYR 0.013 0.001 TYR E 24 PHE 0.005 0.001 PHE L 129 TRP 0.007 0.001 TRP L 134 HIS 0.003 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00350 (33397) covalent geometry : angle 0.46654 (45129) hydrogen bonds : bond 0.07130 ( 2611) hydrogen bonds : angle 3.34425 ( 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 244 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 1.331 Fit side-chains REVERT: C 47 MET cc_start: 0.8542 (mmt) cc_final: 0.7717 (mmt) REVERT: C 78 MET cc_start: 0.8511 (mtt) cc_final: 0.8208 (mtt) REVERT: E 47 MET cc_start: 0.8549 (mmt) cc_final: 0.7733 (mmt) REVERT: F 47 MET cc_start: 0.8530 (mmt) cc_final: 0.7708 (mmt) REVERT: G 78 MET cc_start: 0.8563 (mtt) cc_final: 0.8265 (mtt) REVERT: J 78 MET cc_start: 0.8563 (mtt) cc_final: 0.8270 (mtt) REVERT: P 78 MET cc_start: 0.8568 (mtt) cc_final: 0.8274 (mtt) REVERT: Q 47 MET cc_start: 0.8541 (mmt) cc_final: 0.7718 (mmt) REVERT: S 78 MET cc_start: 0.8588 (mtt) cc_final: 0.8308 (mtt) REVERT: T 78 MET cc_start: 0.8553 (mtt) cc_final: 0.8269 (mtt) REVERT: W 78 MET cc_start: 0.8569 (mtt) cc_final: 0.8285 (mtt) outliers start: 3 outliers final: 3 residues processed: 244 average time/residue: 0.1725 time to fit residues: 74.1692 Evaluate side-chains 244 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain L residue 91 ILE 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: 0.9990 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 333 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117400 restraints weight = 306912.358| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.43 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2608 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= 0.105 Angle : 0.394 5.652 45129 Z= 0.222 Chirality : 0.035 0.107 4895 Planarity : 0.003 0.028 5806 Dihedral : 3.387 13.695 4319 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.73 % Allowed : 13.71 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.13), residues: 3983 helix: 2.74 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.95 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 105 TYR 0.009 0.001 TYR N 24 PHE 0.006 0.001 PHE L 129 TRP 0.003 0.001 TRP D 134 HIS 0.003 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00188 (33397) covalent geometry : angle 0.39384 (45129) hydrogen bonds : bond 0.04863 ( 2611) hydrogen bonds : angle 2.90375 ( 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 338 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 1.266 Fit side-chains REVERT: A 47 MET cc_start: 0.8289 (mmt) cc_final: 0.7556 (mmt) REVERT: B 47 MET cc_start: 0.8107 (mmt) cc_final: 0.7421 (mmt) REVERT: C 47 MET cc_start: 0.8222 (mmt) cc_final: 0.7480 (mmt) REVERT: D 47 MET cc_start: 0.8066 (mmt) cc_final: 0.7424 (mmt) REVERT: E 47 MET cc_start: 0.8282 (mmt) cc_final: 0.7562 (mmt) REVERT: F 47 MET cc_start: 0.8246 (mmt) cc_final: 0.7530 (mmt) REVERT: G 47 MET cc_start: 0.8170 (mmt) cc_final: 0.7441 (mmt) REVERT: G 78 MET cc_start: 0.8392 (mtt) cc_final: 0.8079 (mtt) REVERT: H 47 MET cc_start: 0.8281 (mmt) cc_final: 0.7547 (mmt) REVERT: I 47 MET cc_start: 0.8059 (mmt) cc_final: 0.7438 (mmt) REVERT: J 47 MET cc_start: 0.8098 (mmt) cc_final: 0.7364 (mmt) REVERT: J 78 MET cc_start: 0.8385 (mtt) cc_final: 0.8085 (mtt) REVERT: K 47 MET cc_start: 0.8133 (mmt) cc_final: 0.7434 (mmt) REVERT: L 47 MET cc_start: 0.8126 (mmt) cc_final: 0.7418 (mmt) REVERT: M 47 MET cc_start: 0.8148 (mmt) cc_final: 0.7462 (mmt) REVERT: N 47 MET cc_start: 0.8181 (mmt) cc_final: 0.7474 (mmt) REVERT: O 47 MET cc_start: 0.8081 (mmt) cc_final: 0.7423 (mmt) REVERT: P 47 MET cc_start: 0.8256 (mmt) cc_final: 0.7513 (mmt) REVERT: P 78 MET cc_start: 0.8364 (mtt) cc_final: 0.8051 (mtt) REVERT: Q 47 MET cc_start: 0.8279 (mmt) cc_final: 0.7538 (mmt) REVERT: R 47 MET cc_start: 0.8251 (mmt) cc_final: 0.7539 (mmt) REVERT: S 47 MET cc_start: 0.8171 (mmt) cc_final: 0.7435 (mmt) REVERT: S 78 MET cc_start: 0.8398 (mtt) cc_final: 0.8110 (mtt) REVERT: T 47 MET cc_start: 0.8107 (mmt) cc_final: 0.7418 (mmt) REVERT: T 78 MET cc_start: 0.8403 (mtt) cc_final: 0.8099 (mtt) REVERT: U 47 MET cc_start: 0.8115 (mmt) cc_final: 0.7427 (mmt) REVERT: V 47 MET cc_start: 0.8120 (mmt) cc_final: 0.7442 (mmt) REVERT: W 47 MET cc_start: 0.8160 (mmt) cc_final: 0.7474 (mmt) REVERT: W 78 MET cc_start: 0.8400 (mtt) cc_final: 0.8104 (mtt) REVERT: X 47 MET cc_start: 0.8105 (mmt) cc_final: 0.7424 (mmt) outliers start: 2 outliers final: 0 residues processed: 338 average time/residue: 0.1684 time to fit residues: 101.9352 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 : 1.226 ------------------------------------------------------------------------------- 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: 4.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN C 22 GLN D 22 GLN E 22 GLN F 22 GLN F 76 ASN G 22 GLN H 22 GLN I 22 GLN J 22 GLN K 22 GLN K 76 ASN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110716 restraints weight = 326974.397| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 5.69 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33397 Z= 0.135 Angle : 0.433 6.026 45129 Z= 0.241 Chirality : 0.037 0.108 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.406 12.775 4319 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.70 % Allowed : 13.86 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.13), residues: 3983 helix: 2.68 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.91 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 105 TYR 0.013 0.001 TYR N 24 PHE 0.006 0.001 PHE L 129 TRP 0.006 0.001 TRP D 134 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00275 (33397) covalent geometry : angle 0.43276 (45129) hydrogen bonds : bond 0.06132 ( 2611) hydrogen bonds : angle 3.12085 ( 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 284 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.131 Fit side-chains REVERT: A 47 MET cc_start: 0.8528 (mmt) cc_final: 0.7712 (mmt) REVERT: B 47 MET cc_start: 0.8385 (mmt) cc_final: 0.7641 (mmt) REVERT: C 47 MET cc_start: 0.8440 (mmt) cc_final: 0.7579 (mmt) REVERT: D 47 MET cc_start: 0.8381 (mmt) cc_final: 0.7646 (mmt) REVERT: E 47 MET cc_start: 0.8543 (mmt) cc_final: 0.7731 (mmt) REVERT: F 47 MET cc_start: 0.8432 (mmt) cc_final: 0.7592 (mmt) REVERT: G 47 MET cc_start: 0.8402 (mmt) cc_final: 0.7581 (mmt) REVERT: G 78 MET cc_start: 0.8386 (mtt) cc_final: 0.8087 (mtt) REVERT: H 47 MET cc_start: 0.8548 (mmt) cc_final: 0.7738 (mmt) REVERT: I 47 MET cc_start: 0.8352 (mmt) cc_final: 0.7630 (mmt) REVERT: J 47 MET cc_start: 0.8387 (mmt) cc_final: 0.7539 (mmt) REVERT: J 78 MET cc_start: 0.8389 (mtt) cc_final: 0.8102 (mtt) REVERT: K 47 MET cc_start: 0.8398 (mmt) cc_final: 0.7589 (mmt) REVERT: L 47 MET cc_start: 0.8390 (mmt) cc_final: 0.7567 (mmt) REVERT: L 78 MET cc_start: 0.7986 (mtm) cc_final: 0.7637 (mtt) REVERT: M 47 MET cc_start: 0.8416 (mmt) cc_final: 0.7602 (mmt) REVERT: N 47 MET cc_start: 0.8383 (mmt) cc_final: 0.7572 (mmt) REVERT: O 47 MET cc_start: 0.8407 (mmt) cc_final: 0.7656 (mmt) REVERT: P 78 MET cc_start: 0.8387 (mtt) cc_final: 0.8091 (mtt) REVERT: Q 47 MET cc_start: 0.8522 (mmt) cc_final: 0.7683 (mmt) REVERT: R 47 MET cc_start: 0.8541 (mmt) cc_final: 0.7734 (mmt) REVERT: S 47 MET cc_start: 0.8395 (mmt) cc_final: 0.7568 (mmt) REVERT: S 78 MET cc_start: 0.8461 (mtt) cc_final: 0.8199 (mtt) REVERT: T 47 MET cc_start: 0.8387 (mmt) cc_final: 0.7651 (mmt) REVERT: T 78 MET cc_start: 0.8449 (mtt) cc_final: 0.8174 (mtt) REVERT: U 47 MET cc_start: 0.8412 (mmt) cc_final: 0.7594 (mmt) REVERT: V 47 MET cc_start: 0.8414 (mmt) cc_final: 0.7681 (mmt) REVERT: W 47 MET cc_start: 0.8399 (mmt) cc_final: 0.7653 (mmt) REVERT: W 78 MET cc_start: 0.8393 (mtt) cc_final: 0.8114 (mtt) REVERT: X 47 MET cc_start: 0.8379 (mmt) cc_final: 0.7641 (mmt) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1565 time to fit residues: 79.3124 Evaluate side-chains 283 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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: 5.9990 chunk 278 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN K 22 GLN L 22 GLN M 22 GLN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN T 22 GLN V 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114253 restraints weight = 329722.456| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 5.75 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 33397 Z= 0.110 Angle : 0.396 6.504 45129 Z= 0.223 Chirality : 0.036 0.108 4895 Planarity : 0.003 0.027 5806 Dihedral : 3.360 13.517 4319 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.68 % Allowed : 13.86 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.13), residues: 3983 helix: 2.80 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.89 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 105 TYR 0.011 0.001 TYR W 24 PHE 0.006 0.001 PHE L 129 TRP 0.003 0.001 TRP N 134 HIS 0.003 0.000 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00202 (33397) covalent geometry : angle 0.39640 (45129) hydrogen bonds : bond 0.05173 ( 2611) hydrogen bonds : angle 2.93558 ( 7785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.94 seconds wall clock time: 85 minutes 27.73 seconds (5127.73 seconds total)