Starting phenix.real_space_refine on Tue Aug 26 00:40:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqu_37754/08_2025/8wqu_37754.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.151 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20928 2.51 5 N 5328 2.21 5 O 6384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32736 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "D" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "E" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "G" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "H" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "I" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "J" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "K" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "L" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "M" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "N" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "O" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "P" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "Q" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "R" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "S" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "T" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "U" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "V" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "W" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "X" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 13.06, per 1000 atoms: 0.40 Number of scatterers: 32736 At special positions: 0 Unit cell: (132.956, 132.956, 132.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 72 16.00 O 6384 8.00 N 5328 7.00 C 20928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 12 sheets defined 82.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.663A pdb=" N ASN A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 3.530A pdb=" N PHE A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 132 through 151 removed outlier: 4.019A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'C' and resid 14 through 45 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.525A pdb=" N PHE C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.527A pdb=" N PHE D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 3.542A pdb=" N PHE G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 158 through 171 Processing helix chain 'H' and resid 14 through 45 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 122 removed outlier: 3.783A pdb=" N LEU H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 151 removed outlier: 4.016A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 45 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 122 removed outlier: 3.784A pdb=" N LEU K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'L' and resid 14 through 45 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 122 removed outlier: 3.675A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'M' and resid 14 through 45 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 151 removed outlier: 4.263A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 122 removed outlier: 3.674A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 171 Processing helix chain 'O' and resid 14 through 45 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 122 removed outlier: 3.787A pdb=" N LEU O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 151 removed outlier: 4.624A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 155 Processing helix chain 'P' and resid 158 through 171 Processing helix chain 'Q' and resid 14 through 45 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 3.517A pdb=" N PHE Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 155 Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 122 removed outlier: 3.679A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'S' and resid 14 through 45 Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.551A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR S 130 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 151 removed outlier: 4.024A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 Processing helix chain 'T' and resid 158 through 171 Processing helix chain 'U' and resid 14 through 45 Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 151 removed outlier: 4.369A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 171 Processing helix chain 'W' and resid 14 through 45 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 155 Processing helix chain 'W' and resid 158 through 171 Processing helix chain 'X' and resid 14 through 45 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.474A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 122 removed outlier: 3.788A pdb=" N LEU X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 151 removed outlier: 4.625A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 155 Processing helix chain 'X' and resid 158 through 171 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2550 hydrogen bonds defined for protein. 7626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5856 1.28 - 1.41: 8442 1.41 - 1.54: 18870 1.54 - 1.67: 96 1.67 - 1.81: 144 Bond restraints: 33408 Sorted by residual: bond pdb=" C PHE I 129 " pdb=" O PHE I 129 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.31e-02 5.83e+03 4.60e+01 bond pdb=" C PHE E 129 " pdb=" O PHE E 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE O 129 " pdb=" O PHE O 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE N 129 " pdb=" O PHE N 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 bond pdb=" C PHE F 129 " pdb=" O PHE F 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 ... (remaining 33403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 43569 1.63 - 3.26: 1207 3.26 - 4.90: 239 4.90 - 6.53: 67 6.53 - 8.16: 62 Bond angle restraints: 45144 Sorted by residual: angle pdb=" N TYR A 126 " pdb=" CA TYR A 126 " pdb=" C TYR A 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR Q 126 " pdb=" CA TYR Q 126 " pdb=" C TYR Q 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR D 126 " pdb=" CA TYR D 126 " pdb=" C TYR D 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR C 126 " pdb=" CA TYR C 126 " pdb=" C TYR C 126 " ideal model delta sigma weight residual 113.17 105.21 7.96 1.26e+00 6.30e-01 3.99e+01 angle pdb=" N TYR T 126 " pdb=" CA TYR T 126 " pdb=" C TYR T 126 " ideal model delta sigma weight residual 113.17 105.24 7.93 1.26e+00 6.30e-01 3.96e+01 ... (remaining 45139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17913 16.60 - 33.20: 1699 33.20 - 49.80: 247 49.80 - 66.40: 114 66.40 - 83.00: 67 Dihedral angle restraints: 20040 sinusoidal: 8136 harmonic: 11904 Sorted by residual: dihedral pdb=" C ASP A 124 " pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" CB ASP A 124 " ideal model delta harmonic sigma weight residual -122.60 -139.62 17.02 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C ASP C 124 " pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " ideal model delta harmonic sigma weight residual -122.60 -139.60 17.00 0 2.50e+00 1.60e-01 4.62e+01 dihedral pdb=" C ASP D 124 " pdb=" N ASP D 124 " pdb=" CA ASP D 124 " pdb=" CB ASP D 124 " ideal model delta harmonic sigma weight residual -122.60 -139.59 16.99 0 2.50e+00 1.60e-01 4.62e+01 ... (remaining 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4849 0.168 - 0.336: 23 0.336 - 0.504: 0 0.504 - 0.673: 16 0.673 - 0.841: 8 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA ASP U 124 " pdb=" N ASP U 124 " pdb=" C ASP U 124 " pdb=" CB ASP U 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP A 124 " pdb=" N ASP A 124 " pdb=" C ASP A 124 " pdb=" CB ASP A 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP C 124 " pdb=" N ASP C 124 " pdb=" C ASP C 124 " pdb=" CB ASP C 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 4893 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 123 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLU F 123 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU F 123 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU P 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU P 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP P 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU G 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU G 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP G 124 " -0.023 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 27842 3.20 - 3.77: 48410 3.77 - 4.33: 68676 4.33 - 4.90: 114527 Nonbonded interactions: 259623 Sorted by model distance: nonbonded pdb=" NE2 HIS E 65 " pdb="FE FE E 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS L 65 " pdb="FE FE L 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS A 65 " pdb="FE FE A 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS G 65 " pdb="FE FE G 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.074 2.340 ... (remaining 259618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.340 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 33408 Z= 0.569 Angle : 0.750 8.160 45144 Z= 0.453 Chirality : 0.066 0.841 4896 Planarity : 0.005 0.041 5808 Dihedral : 14.543 82.999 12360 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.12), residues: 3984 helix: 0.10 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -2.65 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 110 TYR 0.033 0.004 TYR M 130 PHE 0.015 0.002 PHE I 129 TRP 0.004 0.002 TRP L 180 HIS 0.005 0.001 HIS G 112 Details of bonding type rmsd covalent geometry : bond 0.00951 (33408) covalent geometry : angle 0.74959 (45144) hydrogen bonds : bond 0.15897 ( 2550) hydrogen bonds : angle 5.66229 ( 7626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 0.925 Fit side-chains REVERT: A 76 ASN cc_start: 0.8166 (p0) cc_final: 0.7507 (p0) REVERT: A 114 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7548 (tttt) REVERT: B 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7406 (p0) REVERT: B 114 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7548 (tttt) REVERT: C 76 ASN cc_start: 0.8077 (p0) cc_final: 0.7413 (p0) REVERT: C 114 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7529 (tttt) REVERT: D 76 ASN cc_start: 0.8169 (p0) cc_final: 0.7533 (p0) REVERT: D 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7521 (tttt) REVERT: E 76 ASN cc_start: 0.8057 (p0) cc_final: 0.7386 (p0) REVERT: F 76 ASN cc_start: 0.8032 (p0) cc_final: 0.7357 (p0) REVERT: F 114 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7534 (tttt) REVERT: G 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: G 114 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7514 (tttt) REVERT: H 76 ASN cc_start: 0.8073 (p0) cc_final: 0.7404 (p0) REVERT: H 114 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7527 (tttt) REVERT: I 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: I 114 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7556 (tttt) REVERT: J 76 ASN cc_start: 0.8087 (p0) cc_final: 0.7423 (p0) REVERT: J 114 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7525 (tttt) REVERT: K 76 ASN cc_start: 0.8090 (p0) cc_final: 0.7417 (p0) REVERT: K 114 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7577 (tttt) REVERT: L 76 ASN cc_start: 0.8059 (p0) cc_final: 0.7397 (p0) REVERT: L 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7538 (tttt) REVERT: M 76 ASN cc_start: 0.8046 (p0) cc_final: 0.7368 (p0) REVERT: M 114 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7533 (tttt) REVERT: N 76 ASN cc_start: 0.8157 (p0) cc_final: 0.7495 (p0) REVERT: N 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7552 (tttt) REVERT: O 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7384 (p0) REVERT: O 114 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7547 (tttt) REVERT: P 76 ASN cc_start: 0.8052 (p0) cc_final: 0.7374 (p0) REVERT: P 114 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7522 (tttt) REVERT: Q 76 ASN cc_start: 0.8045 (p0) cc_final: 0.7370 (p0) REVERT: Q 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7552 (tttt) REVERT: R 76 ASN cc_start: 0.8032 (p0) cc_final: 0.7359 (p0) REVERT: R 114 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7589 (tttt) REVERT: S 76 ASN cc_start: 0.8181 (p0) cc_final: 0.7523 (p0) REVERT: S 114 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7524 (tttt) REVERT: T 76 ASN cc_start: 0.8083 (p0) cc_final: 0.7418 (p0) REVERT: T 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7523 (tttt) REVERT: U 76 ASN cc_start: 0.8048 (p0) cc_final: 0.7364 (p0) REVERT: U 114 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7526 (tttt) REVERT: V 76 ASN cc_start: 0.8067 (p0) cc_final: 0.7404 (p0) REVERT: V 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7543 (tttt) REVERT: W 76 ASN cc_start: 0.8149 (p0) cc_final: 0.7481 (p0) REVERT: W 114 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7556 (tttt) REVERT: X 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7381 (p0) REVERT: X 114 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7531 (tttt) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.5536 time to fit residues: 350.2394 Evaluate side-chains 309 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN C 22 GLN D 22 GLN E 22 GLN F 22 GLN G 22 GLN H 22 GLN I 22 GLN J 22 GLN K 22 GLN M 22 GLN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN S 22 GLN T 22 GLN U 22 GLN V 22 GLN W 22 GLN X 22 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128652 restraints weight = 199281.494| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.37 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.128 Angle : 0.438 4.362 45144 Z= 0.248 Chirality : 0.036 0.113 4896 Planarity : 0.004 0.039 5808 Dihedral : 3.923 12.084 4320 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.38 % 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: 1.49 (0.13), residues: 3984 helix: 1.70 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.70 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 105 TYR 0.016 0.001 TYR D 24 PHE 0.011 0.001 PHE X 129 TRP 0.002 0.001 TRP V 134 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00232 (33408) covalent geometry : angle 0.43763 (45144) hydrogen bonds : bond 0.06578 ( 2550) hydrogen bonds : angle 3.92468 ( 7626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 1.393 Fit side-chains REVERT: A 107 ASN cc_start: 0.8900 (t0) cc_final: 0.8580 (t0) REVERT: A 114 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7608 (tttt) REVERT: B 114 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7651 (tttt) REVERT: D 107 ASN cc_start: 0.8893 (t0) cc_final: 0.8582 (t0) REVERT: D 114 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7598 (tttt) REVERT: E 107 ASN cc_start: 0.8889 (t0) cc_final: 0.8578 (t0) REVERT: E 114 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7623 (tttt) REVERT: F 114 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7621 (tttt) REVERT: G 114 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7589 (tttt) REVERT: H 107 ASN cc_start: 0.8891 (t0) cc_final: 0.8578 (t0) REVERT: H 114 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7617 (tttt) REVERT: I 107 ASN cc_start: 0.8894 (t0) cc_final: 0.8580 (t0) REVERT: I 114 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7599 (tttt) REVERT: J 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7654 (tttt) REVERT: K 107 ASN cc_start: 0.8887 (t0) cc_final: 0.8560 (t0) REVERT: K 114 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7588 (tttt) REVERT: L 107 ASN cc_start: 0.8889 (t0) cc_final: 0.8567 (t0) REVERT: L 114 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7631 (tttt) REVERT: N 107 ASN cc_start: 0.8887 (t0) cc_final: 0.8584 (t0) REVERT: N 114 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7618 (tttt) REVERT: O 114 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7644 (tttt) REVERT: Q 107 ASN cc_start: 0.8887 (t0) cc_final: 0.8572 (t0) REVERT: Q 114 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7617 (tttt) REVERT: R 107 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8553 (t0) REVERT: R 114 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7608 (tttt) REVERT: S 107 ASN cc_start: 0.8909 (t0) cc_final: 0.8603 (t0) REVERT: S 114 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7624 (tttt) REVERT: U 107 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8545 (t0) REVERT: V 107 ASN cc_start: 0.8897 (t0) cc_final: 0.8594 (t0) REVERT: V 114 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7607 (tttt) REVERT: W 107 ASN cc_start: 0.8893 (t0) cc_final: 0.8592 (t0) REVERT: W 114 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7649 (tttt) REVERT: X 114 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7634 (tttt) outliers start: 2 outliers final: 0 residues processed: 455 average time/residue: 0.5883 time to fit residues: 326.8970 Evaluate side-chains 352 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 350 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 196 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 329 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119894 restraints weight = 216744.972| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.40 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33408 Z= 0.181 Angle : 0.496 5.787 45144 Z= 0.276 Chirality : 0.039 0.116 4896 Planarity : 0.004 0.039 5808 Dihedral : 3.925 11.880 4320 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.18 % Allowed : 8.84 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.13), residues: 3984 helix: 1.81 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.44 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 110 TYR 0.017 0.002 TYR P 24 PHE 0.013 0.002 PHE O 129 TRP 0.003 0.001 TRP A 180 HIS 0.003 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00388 (33408) covalent geometry : angle 0.49632 (45144) hydrogen bonds : bond 0.08953 ( 2550) hydrogen bonds : angle 3.99927 ( 7626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 394 time to evaluate : 1.444 Fit side-chains REVERT: A 76 ASN cc_start: 0.7731 (p0) cc_final: 0.7375 (p0) REVERT: A 114 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7926 (tttt) REVERT: B 76 ASN cc_start: 0.7704 (p0) cc_final: 0.7352 (p0) REVERT: B 114 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7959 (tttt) REVERT: C 76 ASN cc_start: 0.7687 (p0) cc_final: 0.7331 (p0) REVERT: C 107 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8646 (t0) REVERT: D 76 ASN cc_start: 0.7728 (p0) cc_final: 0.7371 (p0) REVERT: D 114 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7935 (tttt) REVERT: E 76 ASN cc_start: 0.7728 (p0) cc_final: 0.7372 (p0) REVERT: E 114 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7939 (tttt) REVERT: F 76 ASN cc_start: 0.7679 (p0) cc_final: 0.7319 (p0) REVERT: F 114 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7923 (tttt) REVERT: G 76 ASN cc_start: 0.7691 (p0) cc_final: 0.7341 (p0) REVERT: G 114 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7933 (tttt) REVERT: H 76 ASN cc_start: 0.7710 (p0) cc_final: 0.7351 (p0) REVERT: H 114 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7944 (tttt) REVERT: I 76 ASN cc_start: 0.7692 (p0) cc_final: 0.7343 (p0) REVERT: I 114 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7929 (tttt) REVERT: J 76 ASN cc_start: 0.7688 (p0) cc_final: 0.7342 (p0) REVERT: J 114 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7939 (tttt) REVERT: K 76 ASN cc_start: 0.7711 (p0) cc_final: 0.7360 (p0) REVERT: K 114 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7926 (tttt) REVERT: L 76 ASN cc_start: 0.7702 (p0) cc_final: 0.7359 (p0) REVERT: L 114 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7941 (tttt) REVERT: M 76 ASN cc_start: 0.7688 (p0) cc_final: 0.7199 (p0) REVERT: N 76 ASN cc_start: 0.7703 (p0) cc_final: 0.7357 (p0) REVERT: N 114 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7934 (tttt) REVERT: O 76 ASN cc_start: 0.7681 (p0) cc_final: 0.7330 (p0) REVERT: O 114 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7935 (tttt) REVERT: P 76 ASN cc_start: 0.7685 (p0) cc_final: 0.7328 (p0) REVERT: Q 76 ASN cc_start: 0.7723 (p0) cc_final: 0.7364 (p0) REVERT: Q 114 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7922 (tttt) REVERT: R 76 ASN cc_start: 0.7710 (p0) cc_final: 0.7353 (p0) REVERT: R 107 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8553 (t0) REVERT: R 114 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7930 (tttt) REVERT: S 76 ASN cc_start: 0.7677 (p0) cc_final: 0.7332 (p0) REVERT: S 114 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7942 (tttt) REVERT: T 76 ASN cc_start: 0.7695 (p0) cc_final: 0.7341 (p0) REVERT: U 76 ASN cc_start: 0.7696 (p0) cc_final: 0.7338 (p0) REVERT: U 107 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8551 (t0) REVERT: V 76 ASN cc_start: 0.7709 (p0) cc_final: 0.7352 (p0) REVERT: V 114 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7942 (tttt) REVERT: W 76 ASN cc_start: 0.7708 (p0) cc_final: 0.7355 (p0) REVERT: W 114 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7954 (tttt) REVERT: X 76 ASN cc_start: 0.7719 (p0) cc_final: 0.7360 (p0) REVERT: X 114 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7930 (tttt) outliers start: 32 outliers final: 24 residues processed: 402 average time/residue: 0.6151 time to fit residues: 303.2386 Evaluate side-chains 396 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 369 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 84 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 372 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126169 restraints weight = 205959.897| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.47 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.126 Angle : 0.417 5.401 45144 Z= 0.234 Chirality : 0.036 0.115 4896 Planarity : 0.003 0.037 5808 Dihedral : 3.685 12.068 4320 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.06 % Allowed : 9.04 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.49 (0.13), residues: 3984 helix: 2.37 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.16 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 110 TYR 0.015 0.001 TYR M 24 PHE 0.009 0.001 PHE X 129 TRP 0.002 0.001 TRP S 180 HIS 0.005 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00230 (33408) covalent geometry : angle 0.41699 (45144) hydrogen bonds : bond 0.06706 ( 2550) hydrogen bonds : angle 3.71029 ( 7626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 1.351 Fit side-chains REVERT: A 107 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8479 (t0) REVERT: B 107 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8433 (t0) REVERT: D 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8452 (t0) REVERT: F 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8431 (t0) REVERT: G 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8424 (t0) REVERT: I 107 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8463 (t0) REVERT: J 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (t0) REVERT: L 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (t0) REVERT: M 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8452 (t0) REVERT: N 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8447 (t0) REVERT: O 107 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8454 (t0) REVERT: P 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (t0) REVERT: Q 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8465 (t0) REVERT: R 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8441 (t0) REVERT: S 107 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8464 (t0) REVERT: T 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8435 (t0) REVERT: U 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8439 (t0) REVERT: W 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8466 (t0) REVERT: X 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8427 (t0) outliers start: 56 outliers final: 0 residues processed: 399 average time/residue: 0.5528 time to fit residues: 275.6949 Evaluate side-chains 380 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 360 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 188 optimal weight: 0.9980 chunk 238 optimal weight: 9.9990 chunk 381 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124237 restraints weight = 204122.802| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.43 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 33408 Z= 0.135 Angle : 0.429 5.825 45144 Z= 0.240 Chirality : 0.037 0.113 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.652 12.565 4320 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.60 % Allowed : 10.16 % Favored : 88.23 % 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: 2.64 (0.13), residues: 3984 helix: 2.41 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.93 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 110 TYR 0.015 0.001 TYR P 24 PHE 0.010 0.001 PHE N 129 TRP 0.002 0.001 TRP A 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00259 (33408) covalent geometry : angle 0.42925 (45144) hydrogen bonds : bond 0.07173 ( 2550) hydrogen bonds : angle 3.73150 ( 7626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 366 time to evaluate : 1.365 Fit side-chains REVERT: B 107 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8443 (t0) REVERT: E 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (t0) REVERT: F 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8444 (t0) REVERT: H 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8449 (t0) REVERT: K 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8453 (t0) REVERT: O 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (t0) REVERT: P 107 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8437 (t0) REVERT: R 107 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8430 (t0) REVERT: T 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (t0) REVERT: U 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8415 (t0) REVERT: V 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8474 (t0) REVERT: X 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8438 (t0) outliers start: 37 outliers final: 0 residues processed: 382 average time/residue: 0.5151 time to fit residues: 248.6818 Evaluate side-chains 372 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 360 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 327 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 381 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 371 optimal weight: 0.1980 chunk 175 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131328 restraints weight = 206529.576| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.50 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 33408 Z= 0.107 Angle : 0.391 5.802 45144 Z= 0.218 Chirality : 0.036 0.114 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.492 12.174 4320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.32 % Allowed : 10.59 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.13), residues: 3984 helix: 2.75 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.72 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.014 0.001 TYR N 24 PHE 0.008 0.001 PHE X 129 TRP 0.001 0.000 TRP A 180 HIS 0.004 0.001 HIS V 39 Details of bonding type rmsd covalent geometry : bond 0.00187 (33408) covalent geometry : angle 0.39111 (45144) hydrogen bonds : bond 0.05584 ( 2550) hydrogen bonds : angle 3.52438 ( 7626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 374 time to evaluate : 1.287 Fit side-chains REVERT: A 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 107 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8441 (t0) REVERT: D 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (t0) REVERT: E 107 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8503 (t0) REVERT: F 107 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8478 (t0) REVERT: G 107 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8463 (t0) REVERT: H 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8491 (t0) REVERT: I 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8485 (t0) REVERT: J 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8447 (t0) REVERT: K 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8486 (t0) REVERT: L 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (t0) REVERT: M 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8481 (t0) REVERT: N 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8478 (t0) REVERT: O 107 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8464 (t0) REVERT: P 107 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (t0) REVERT: Q 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8481 (t0) REVERT: R 107 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8478 (t0) REVERT: S 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8479 (t0) REVERT: T 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8465 (t0) REVERT: U 107 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8465 (t0) REVERT: V 107 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8509 (t0) REVERT: W 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8493 (t0) REVERT: X 107 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (t0) outliers start: 24 outliers final: 0 residues processed: 398 average time/residue: 0.5628 time to fit residues: 282.5504 Evaluate side-chains 361 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 319 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 348 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124521 restraints weight = 215641.922| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.50 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 33408 Z= 0.136 Angle : 0.426 6.004 45144 Z= 0.238 Chirality : 0.037 0.124 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.576 12.834 4320 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.52 % Allowed : 12.25 % Favored : 86.23 % 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: 2.89 (0.13), residues: 3984 helix: 2.55 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.62 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.015 0.002 TYR G 24 PHE 0.010 0.001 PHE F 129 TRP 0.002 0.001 TRP S 180 HIS 0.004 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00263 (33408) covalent geometry : angle 0.42570 (45144) hydrogen bonds : bond 0.07126 ( 2550) hydrogen bonds : angle 3.70679 ( 7626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 358 time to evaluate : 1.325 Fit side-chains REVERT: A 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8469 (t0) REVERT: B 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8424 (t0) REVERT: C 107 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8456 (t0) REVERT: D 107 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (t0) REVERT: E 107 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8449 (t0) REVERT: F 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (t0) REVERT: G 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8425 (t0) REVERT: H 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (t0) REVERT: I 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8442 (t0) REVERT: J 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8415 (t0) REVERT: K 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8442 (t0) REVERT: L 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8448 (t0) REVERT: M 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8446 (t0) REVERT: N 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8448 (t0) REVERT: O 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (t0) REVERT: P 107 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8416 (t0) REVERT: Q 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8468 (t0) REVERT: R 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8421 (t0) REVERT: S 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8439 (t0) REVERT: T 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8443 (t0) REVERT: U 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8416 (t0) REVERT: V 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8457 (t0) REVERT: W 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8439 (t0) REVERT: X 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8436 (t0) outliers start: 30 outliers final: 0 residues processed: 386 average time/residue: 0.5107 time to fit residues: 248.9113 Evaluate side-chains 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 350 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 317 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125384 restraints weight = 214613.019| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.50 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.130 Angle : 0.418 5.970 45144 Z= 0.233 Chirality : 0.037 0.120 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.565 12.912 4320 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.58 % Allowed : 12.42 % Favored : 86.01 % 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: 2.93 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.52 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.015 0.001 TYR M 24 PHE 0.010 0.001 PHE F 129 TRP 0.001 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00245 (33408) covalent geometry : angle 0.41773 (45144) hydrogen bonds : bond 0.06884 ( 2550) hydrogen bonds : angle 3.69742 ( 7626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 1.244 Fit side-chains REVERT: A 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8472 (t0) REVERT: B 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8434 (t0) REVERT: C 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8466 (t0) REVERT: D 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (t0) REVERT: E 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (t0) REVERT: F 107 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8448 (t0) REVERT: G 107 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8424 (t0) REVERT: H 107 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8443 (t0) REVERT: I 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8456 (t0) REVERT: J 107 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8415 (t0) REVERT: K 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (t0) REVERT: L 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8449 (t0) REVERT: M 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8434 (t0) REVERT: N 107 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8439 (t0) REVERT: O 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8438 (t0) REVERT: P 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8436 (t0) REVERT: Q 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8470 (t0) REVERT: R 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8425 (t0) REVERT: S 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8428 (t0) REVERT: T 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (t0) REVERT: U 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8429 (t0) REVERT: V 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8458 (t0) REVERT: W 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8440 (t0) REVERT: X 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8435 (t0) outliers start: 32 outliers final: 0 residues processed: 373 average time/residue: 0.4799 time to fit residues: 227.9372 Evaluate side-chains 372 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 348 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 18 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123835 restraints weight = 210879.272| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.36 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33408 Z= 0.143 Angle : 0.437 5.955 45144 Z= 0.243 Chirality : 0.037 0.120 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.631 13.117 4320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.55 % Allowed : 12.44 % Favored : 86.01 % 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: 2.81 (0.13), residues: 3984 helix: 2.48 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.61 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.015 0.002 TYR V 24 PHE 0.010 0.001 PHE F 129 TRP 0.002 0.001 TRP A 180 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00282 (33408) covalent geometry : angle 0.43662 (45144) hydrogen bonds : bond 0.07516 ( 2550) hydrogen bonds : angle 3.77186 ( 7626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 359 time to evaluate : 1.435 Fit side-chains REVERT: A 107 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8561 (t0) REVERT: B 107 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8531 (t0) REVERT: C 107 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8500 (t0) REVERT: D 107 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8542 (t0) REVERT: E 107 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8536 (t0) REVERT: F 107 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8538 (t0) REVERT: G 107 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8501 (t0) REVERT: H 107 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8532 (t0) REVERT: I 107 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (t0) REVERT: J 107 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8511 (t0) REVERT: K 107 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8516 (t0) REVERT: L 107 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8529 (t0) REVERT: M 107 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8523 (t0) REVERT: N 107 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8526 (t0) REVERT: O 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8527 (t0) REVERT: P 107 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8517 (t0) REVERT: Q 107 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (t0) REVERT: R 107 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (t0) REVERT: S 107 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8539 (t0) REVERT: T 107 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (t0) REVERT: U 107 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8515 (t0) REVERT: V 107 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8533 (t0) REVERT: W 107 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8528 (t0) REVERT: X 107 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8539 (t0) outliers start: 31 outliers final: 0 residues processed: 388 average time/residue: 0.4980 time to fit residues: 244.9812 Evaluate side-chains 383 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 359 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 261 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 274 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122382 restraints weight = 190916.679| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.27 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33408 Z= 0.148 Angle : 0.444 6.069 45144 Z= 0.247 Chirality : 0.037 0.121 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.662 13.269 4320 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.41 % Allowed : 12.61 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.13), residues: 3984 helix: 2.45 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.64 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.015 0.002 TYR O 24 PHE 0.011 0.001 PHE E 129 TRP 0.002 0.001 TRP B 180 HIS 0.003 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00296 (33408) covalent geometry : angle 0.44432 (45144) hydrogen bonds : bond 0.07711 ( 2550) hydrogen bonds : angle 3.81215 ( 7626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 361 time to evaluate : 1.305 Fit side-chains REVERT: A 107 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8503 (t0) REVERT: B 107 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8457 (t0) REVERT: C 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8428 (t0) REVERT: D 107 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8476 (t0) REVERT: E 107 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8474 (t0) REVERT: F 107 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (t0) REVERT: G 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (t0) REVERT: H 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8458 (t0) REVERT: I 107 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8486 (t0) REVERT: J 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8456 (t0) REVERT: K 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8454 (t0) REVERT: L 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (t0) REVERT: M 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8462 (t0) REVERT: N 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (t0) REVERT: O 107 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8453 (t0) REVERT: P 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8447 (t0) REVERT: Q 107 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8493 (t0) REVERT: R 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (t0) REVERT: S 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (t0) REVERT: T 107 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8463 (t0) REVERT: U 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8447 (t0) REVERT: V 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8464 (t0) REVERT: W 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8460 (t0) REVERT: X 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8469 (t0) outliers start: 26 outliers final: 0 residues processed: 387 average time/residue: 0.4623 time to fit residues: 228.4654 Evaluate side-chains 385 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123812 restraints weight = 198581.372| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.25 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33408 Z= 0.143 Angle : 0.437 5.968 45144 Z= 0.243 Chirality : 0.037 0.120 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.654 13.343 4320 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.44 % Allowed : 12.70 % Favored : 85.87 % 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: 2.80 (0.13), residues: 3984 helix: 2.47 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.61 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 105 TYR 0.014 0.002 TYR P 24 PHE 0.010 0.001 PHE F 129 TRP 0.002 0.001 TRP F 180 HIS 0.003 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00283 (33408) covalent geometry : angle 0.43683 (45144) hydrogen bonds : bond 0.07505 ( 2550) hydrogen bonds : angle 3.79182 ( 7626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7544.14 seconds wall clock time: 130 minutes 30.62 seconds (7830.62 seconds total)