Starting phenix.real_space_refine on Thu May 29 11:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqu_37754/05_2025/8wqu_37754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqu_37754/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqu_37754/05_2025/8wqu_37754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqu_37754/05_2025/8wqu_37754.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqu_37754/05_2025/8wqu_37754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqu_37754/05_2025/8wqu_37754.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 30.77, per 1000 atoms: 0.94 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: 8.36 Conformation dependent library (CDL) restraints added in 7.5 seconds 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 12 sheets defined 82.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 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: 10.45 Time building geometry restraints manager: 9.64 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 85.480 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.200 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:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.002 TRP L 180 HIS 0.005 0.001 HIS G 112 PHE 0.015 0.002 PHE I 129 TYR 0.033 0.004 TYR M 130 ARG 0.009 0.001 ARG J 110 Details of bonding type rmsd hydrogen bonds : bond 0.15897 ( 2550) hydrogen bonds : angle 5.66229 ( 7626) covalent geometry : bond 0.00951 (33408) covalent geometry : angle 0.74959 (45144) *********************** 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 : 3.593 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: 1.2179 time to fit residues: 771.0571 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 : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 7.9990 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.148088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125687 restraints weight = 192050.895| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.28 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1487 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= 0.140 Angle : 0.452 4.404 45144 Z= 0.256 Chirality : 0.036 0.112 4896 Planarity : 0.004 0.039 5808 Dihedral : 3.985 11.940 4320 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.13), residues: 3984 helix: 1.63 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.75 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP V 134 HIS 0.003 0.001 HIS D 39 PHE 0.013 0.001 PHE E 129 TYR 0.016 0.001 TYR A 24 ARG 0.004 0.000 ARG P 105 Details of bonding type rmsd hydrogen bonds : bond 0.07330 ( 2550) hydrogen bonds : angle 3.98353 ( 7626) covalent geometry : bond 0.00262 (33408) covalent geometry : angle 0.45246 (45144) *********************** 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 433 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 6.710 Fit side-chains REVERT: A 114 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7717 (tttt) REVERT: B 114 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7724 (tttt) REVERT: C 114 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7721 (tttt) REVERT: D 114 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7705 (tttt) REVERT: E 114 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7725 (tttt) REVERT: F 114 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7729 (tttt) REVERT: G 114 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7704 (tttt) REVERT: H 114 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7719 (tttt) REVERT: I 114 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7717 (tttt) REVERT: J 114 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7720 (tttt) REVERT: K 114 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7706 (tttt) REVERT: L 114 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7730 (tttt) REVERT: M 114 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7737 (tttt) REVERT: N 114 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7720 (tttt) REVERT: O 114 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7729 (tttt) REVERT: P 114 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7719 (tttt) REVERT: Q 114 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7713 (tttt) REVERT: R 107 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (t0) REVERT: R 114 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7731 (tttt) REVERT: S 114 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7723 (tttt) REVERT: T 114 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7737 (tttt) REVERT: U 107 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8585 (t0) REVERT: U 114 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7712 (tttt) REVERT: V 114 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7720 (tttt) REVERT: W 114 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7737 (tttt) REVERT: X 114 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7736 (tttt) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 1.2161 time to fit residues: 649.0415 Evaluate side-chains 350 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 3.863 ------------------------------------------------------------------------------- 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 152 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 350 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.151077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128757 restraints weight = 200672.869| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.45 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 33408 Z= 0.118 Angle : 0.408 5.433 45144 Z= 0.229 Chirality : 0.036 0.120 4896 Planarity : 0.003 0.038 5808 Dihedral : 3.647 11.764 4320 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 9.32 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.13), residues: 3984 helix: 2.27 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.34 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 180 HIS 0.005 0.001 HIS E 39 PHE 0.009 0.001 PHE X 129 TYR 0.015 0.001 TYR N 24 ARG 0.004 0.001 ARG P 105 Details of bonding type rmsd hydrogen bonds : bond 0.06285 ( 2550) hydrogen bonds : angle 3.66387 ( 7626) covalent geometry : bond 0.00211 (33408) covalent geometry : angle 0.40814 (45144) *********************** 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 413 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 388 time to evaluate : 3.632 Fit side-chains REVERT: B 76 ASN cc_start: 0.7040 (p0) cc_final: 0.6665 (p0) REVERT: H 76 ASN cc_start: 0.7082 (p0) cc_final: 0.6719 (p0) REVERT: I 114 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7568 (tttt) REVERT: N 76 ASN cc_start: 0.7067 (p0) cc_final: 0.6670 (p0) REVERT: T 76 ASN cc_start: 0.7064 (p0) cc_final: 0.6699 (p0) REVERT: U 107 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8474 (t0) REVERT: V 76 ASN cc_start: 0.7058 (p0) cc_final: 0.6695 (p0) outliers start: 25 outliers final: 0 residues processed: 389 average time/residue: 1.1863 time to fit residues: 564.1629 Evaluate side-chains 323 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 107 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 132 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 335 optimal weight: 0.8980 chunk 322 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123605 restraints weight = 209057.466| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.50 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 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 = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1800 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= 0.141 Angle : 0.433 5.798 45144 Z= 0.243 Chirality : 0.037 0.121 4896 Planarity : 0.003 0.037 5808 Dihedral : 3.677 12.254 4320 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.59 % Allowed : 11.46 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.13), residues: 3984 helix: 2.30 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.08 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 180 HIS 0.004 0.001 HIS G 39 PHE 0.011 0.001 PHE F 129 TYR 0.015 0.002 TYR X 24 ARG 0.003 0.001 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.07356 ( 2550) hydrogen bonds : angle 3.77252 ( 7626) covalent geometry : bond 0.00276 (33408) covalent geometry : angle 0.43263 (45144) *********************** 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 367 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 364 time to evaluate : 3.683 Fit side-chains REVERT: B 76 ASN cc_start: 0.7255 (p0) cc_final: 0.6810 (p0) REVERT: H 76 ASN cc_start: 0.7343 (p0) cc_final: 0.6919 (p0) REVERT: N 76 ASN cc_start: 0.7288 (p0) cc_final: 0.6846 (p0) REVERT: R 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8430 (t0) REVERT: T 76 ASN cc_start: 0.7293 (p0) cc_final: 0.6873 (p0) REVERT: U 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8412 (t0) REVERT: V 76 ASN cc_start: 0.7304 (p0) cc_final: 0.6878 (p0) outliers start: 3 outliers final: 0 residues processed: 366 average time/residue: 1.0333 time to fit residues: 481.9272 Evaluate side-chains 355 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 122 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 339 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.151344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129160 restraints weight = 206722.829| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.32 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33408 Z= 0.114 Angle : 0.398 5.486 45144 Z= 0.222 Chirality : 0.036 0.113 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.540 12.226 4320 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.32 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.13), residues: 3984 helix: 2.54 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.76 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 180 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.001 PHE F 129 TYR 0.014 0.001 TYR D 24 ARG 0.003 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 2550) hydrogen bonds : angle 3.61216 ( 7626) covalent geometry : bond 0.00201 (33408) covalent geometry : angle 0.39754 (45144) *********************** 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 362 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 347 time to evaluate : 3.594 Fit side-chains REVERT: B 76 ASN cc_start: 0.7088 (p0) cc_final: 0.6613 (p0) REVERT: B 107 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 107 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8464 (t0) REVERT: F 107 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8484 (t0) REVERT: G 107 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8476 (t0) REVERT: H 76 ASN cc_start: 0.7171 (p0) cc_final: 0.6700 (p0) REVERT: J 107 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8465 (t0) REVERT: N 76 ASN cc_start: 0.7127 (p0) cc_final: 0.6658 (p0) REVERT: N 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8491 (t0) REVERT: O 107 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8484 (t0) REVERT: P 107 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8487 (t0) REVERT: R 107 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8483 (t0) REVERT: T 76 ASN cc_start: 0.7086 (p0) cc_final: 0.6612 (p0) REVERT: T 107 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8489 (t0) REVERT: U 107 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8473 (t0) REVERT: V 76 ASN cc_start: 0.7100 (p0) cc_final: 0.6624 (p0) REVERT: X 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8482 (t0) outliers start: 15 outliers final: 3 residues processed: 362 average time/residue: 0.9458 time to fit residues: 438.3373 Evaluate side-chains 351 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 336 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain R residue 93 SER 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 X residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 288 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 357 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 361 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 343 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 = 0.3680 r_free = 0.3680 target = 0.142199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119884 restraints weight = 215511.739| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.37 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 33408 Z= 0.179 Angle : 0.484 5.875 45144 Z= 0.268 Chirality : 0.039 0.126 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.781 12.999 4320 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 10.81 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.13), residues: 3984 helix: 2.25 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.83 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 180 HIS 0.003 0.001 HIS K 39 PHE 0.011 0.002 PHE F 129 TYR 0.017 0.002 TYR I 24 ARG 0.004 0.001 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.08873 ( 2550) hydrogen bonds : angle 3.92662 ( 7626) covalent geometry : bond 0.00386 (33408) covalent geometry : angle 0.48389 (45144) *********************** 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 432 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 3.830 Fit side-chains REVERT: A 107 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8578 (t0) REVERT: B 76 ASN cc_start: 0.7716 (p0) cc_final: 0.7145 (p0) REVERT: B 107 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8543 (t0) REVERT: C 76 ASN cc_start: 0.7707 (p0) cc_final: 0.7395 (p0) REVERT: C 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (t0) REVERT: D 107 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8550 (t0) REVERT: E 107 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (t0) REVERT: F 107 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8539 (t0) REVERT: G 107 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8536 (t0) REVERT: H 76 ASN cc_start: 0.7728 (p0) cc_final: 0.7175 (p0) REVERT: H 107 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8533 (t0) REVERT: I 107 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8582 (t0) REVERT: K 107 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8544 (t0) REVERT: L 76 ASN cc_start: 0.7703 (p0) cc_final: 0.7408 (p0) REVERT: L 107 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8555 (t0) REVERT: M 107 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8555 (t0) REVERT: N 76 ASN cc_start: 0.7714 (p0) cc_final: 0.7151 (p0) REVERT: O 107 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8521 (t0) REVERT: P 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8529 (t0) REVERT: Q 76 ASN cc_start: 0.7687 (p0) cc_final: 0.7388 (p0) REVERT: Q 107 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8583 (t0) REVERT: R 107 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8538 (t0) REVERT: S 107 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8561 (t0) REVERT: T 76 ASN cc_start: 0.7670 (p0) cc_final: 0.7115 (p0) REVERT: T 107 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8537 (t0) REVERT: U 107 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8517 (t0) REVERT: V 76 ASN cc_start: 0.7692 (p0) cc_final: 0.7127 (p0) REVERT: V 107 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8542 (t0) REVERT: W 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8569 (t0) REVERT: X 107 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (t0) outliers start: 41 outliers final: 18 residues processed: 418 average time/residue: 1.0206 time to fit residues: 538.8527 Evaluate side-chains 401 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 361 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 111 ASP 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 V residue 111 ASP Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain W residue 111 ASP 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 207 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 363 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 267 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.145831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123809 restraints weight = 190198.204| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.18 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 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 = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1791 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= 0.144 Angle : 0.436 5.620 45144 Z= 0.244 Chirality : 0.037 0.116 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.695 13.071 4320 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.72 % Allowed : 11.01 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.13), residues: 3984 helix: 2.41 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.71 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 180 HIS 0.003 0.001 HIS K 39 PHE 0.010 0.001 PHE F 129 TYR 0.015 0.002 TYR D 24 ARG 0.003 0.001 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.07574 ( 2550) hydrogen bonds : angle 3.79864 ( 7626) covalent geometry : bond 0.00283 (33408) covalent geometry : angle 0.43601 (45144) *********************** 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 400 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 3.651 Fit side-chains REVERT: A 107 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8563 (t0) REVERT: B 76 ASN cc_start: 0.7503 (p0) cc_final: 0.6948 (p0) REVERT: B 107 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (t0) REVERT: C 107 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8509 (t0) REVERT: D 107 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8545 (t0) REVERT: E 107 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8544 (t0) REVERT: F 107 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (t0) REVERT: G 107 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8515 (t0) REVERT: H 76 ASN cc_start: 0.7513 (p0) cc_final: 0.6977 (p0) REVERT: H 107 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (t0) REVERT: I 107 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8564 (t0) REVERT: J 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8519 (t0) REVERT: K 107 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (t0) REVERT: L 107 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8534 (t0) REVERT: M 107 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8529 (t0) REVERT: N 76 ASN cc_start: 0.7514 (p0) cc_final: 0.6954 (p0) REVERT: N 107 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8535 (t0) REVERT: O 107 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (t0) REVERT: P 107 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8528 (t0) REVERT: Q 107 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8562 (t0) REVERT: R 107 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8515 (t0) REVERT: S 107 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8551 (t0) REVERT: T 76 ASN cc_start: 0.7480 (p0) cc_final: 0.6942 (p0) REVERT: T 107 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8518 (t0) REVERT: U 107 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8509 (t0) REVERT: V 76 ASN cc_start: 0.7505 (p0) cc_final: 0.6957 (p0) REVERT: V 107 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8539 (t0) REVERT: W 107 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8535 (t0) REVERT: X 107 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8520 (t0) outliers start: 37 outliers final: 3 residues processed: 390 average time/residue: 0.9679 time to fit residues: 481.0785 Evaluate side-chains 388 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 361 time to evaluate : 3.609 ------------------------------------------------------------------------------- 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 93 SER 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 93 SER Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 93 SER 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 188 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 327 optimal weight: 0.0370 chunk 38 optimal weight: 7.9990 chunk 172 optimal weight: 0.4980 chunk 358 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.5064 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125818 restraints weight = 205530.715| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.44 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2010 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 : 0.413 5.684 45144 Z= 0.231 Chirality : 0.036 0.117 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.596 12.960 4320 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.75 % Allowed : 10.98 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.57 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 180 HIS 0.004 0.001 HIS Q 39 PHE 0.010 0.001 PHE F 129 TYR 0.015 0.001 TYR M 24 ARG 0.003 0.000 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.06727 ( 2550) hydrogen bonds : angle 3.68025 ( 7626) covalent geometry : bond 0.00236 (33408) covalent geometry : angle 0.41268 (45144) *********************** 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 378 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 3.600 Fit side-chains REVERT: A 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8462 (t0) REVERT: B 76 ASN cc_start: 0.7236 (p0) cc_final: 0.6736 (p0) REVERT: B 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8438 (t0) REVERT: C 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8435 (t0) REVERT: D 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8443 (t0) REVERT: E 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (t0) REVERT: F 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8453 (t0) REVERT: G 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (t0) REVERT: H 76 ASN cc_start: 0.7299 (p0) cc_final: 0.6780 (p0) REVERT: H 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8461 (t0) REVERT: I 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8469 (t0) REVERT: J 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8432 (t0) REVERT: K 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8446 (t0) REVERT: L 107 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8447 (t0) REVERT: M 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8444 (t0) REVERT: N 76 ASN cc_start: 0.7266 (p0) cc_final: 0.6736 (p0) REVERT: N 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8454 (t0) REVERT: O 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (t0) REVERT: P 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8456 (t0) REVERT: Q 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (t0) REVERT: R 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8427 (t0) REVERT: S 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8449 (t0) REVERT: T 76 ASN cc_start: 0.7194 (p0) cc_final: 0.6673 (p0) REVERT: T 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8443 (t0) REVERT: U 107 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8429 (t0) REVERT: V 76 ASN cc_start: 0.7231 (p0) cc_final: 0.6709 (p0) REVERT: V 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (t0) REVERT: W 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8454 (t0) REVERT: X 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8442 (t0) outliers start: 38 outliers final: 13 residues processed: 368 average time/residue: 0.9105 time to fit residues: 429.5685 Evaluate side-chains 377 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 93 SER 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 F residue 111 ASP Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 111 ASP 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 93 SER Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 93 SER 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 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 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.139391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117216 restraints weight = 206606.835| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.37 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33408 Z= 0.201 Angle : 0.510 5.854 45144 Z= 0.281 Chirality : 0.040 0.128 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.856 13.346 4320 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.63 % Allowed : 11.09 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.13), residues: 3984 helix: 2.21 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.78 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 180 HIS 0.003 0.001 HIS X 112 PHE 0.011 0.002 PHE F 129 TYR 0.017 0.002 TYR V 24 ARG 0.004 0.001 ARG T 110 Details of bonding type rmsd hydrogen bonds : bond 0.09433 ( 2550) hydrogen bonds : angle 3.99353 ( 7626) covalent geometry : bond 0.00448 (33408) covalent geometry : angle 0.50981 (45144) *********************** 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 409 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 375 time to evaluate : 3.706 Fit side-chains REVERT: A 76 ASN cc_start: 0.7647 (p0) cc_final: 0.7334 (p0) REVERT: A 107 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 76 ASN cc_start: 0.7646 (p0) cc_final: 0.7073 (p0) REVERT: B 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8464 (t0) REVERT: C 76 ASN cc_start: 0.7628 (p0) cc_final: 0.7299 (p0) REVERT: C 107 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8461 (t0) REVERT: D 76 ASN cc_start: 0.7651 (p0) cc_final: 0.7338 (p0) REVERT: D 107 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8492 (t0) REVERT: E 76 ASN cc_start: 0.7649 (p0) cc_final: 0.7338 (p0) REVERT: E 107 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8456 (t0) REVERT: F 76 ASN cc_start: 0.7621 (p0) cc_final: 0.7301 (p0) REVERT: F 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8475 (t0) REVERT: G 76 ASN cc_start: 0.7614 (p0) cc_final: 0.7299 (p0) REVERT: G 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8475 (t0) REVERT: H 76 ASN cc_start: 0.7653 (p0) cc_final: 0.7094 (p0) REVERT: H 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8471 (t0) REVERT: I 76 ASN cc_start: 0.7606 (p0) cc_final: 0.7288 (p0) REVERT: I 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8510 (t0) REVERT: J 76 ASN cc_start: 0.7631 (p0) cc_final: 0.7318 (p0) REVERT: J 107 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (t0) REVERT: K 76 ASN cc_start: 0.7637 (p0) cc_final: 0.7321 (p0) REVERT: K 107 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8470 (t0) REVERT: L 76 ASN cc_start: 0.7633 (p0) cc_final: 0.7329 (p0) REVERT: L 107 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8478 (t0) REVERT: M 76 ASN cc_start: 0.7630 (p0) cc_final: 0.7325 (p0) REVERT: M 107 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8479 (t0) REVERT: N 76 ASN cc_start: 0.7657 (p0) cc_final: 0.7086 (p0) REVERT: N 107 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8480 (t0) REVERT: O 76 ASN cc_start: 0.7598 (p0) cc_final: 0.7267 (p0) REVERT: O 107 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8451 (t0) REVERT: P 76 ASN cc_start: 0.7600 (p0) cc_final: 0.7297 (p0) REVERT: P 107 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8461 (t0) REVERT: Q 76 ASN cc_start: 0.7629 (p0) cc_final: 0.7311 (p0) REVERT: Q 107 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8528 (t0) REVERT: R 76 ASN cc_start: 0.7670 (p0) cc_final: 0.7366 (p0) REVERT: R 107 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8481 (t0) REVERT: S 107 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8498 (t0) REVERT: T 76 ASN cc_start: 0.7640 (p0) cc_final: 0.7081 (p0) REVERT: T 107 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8468 (t0) REVERT: U 76 ASN cc_start: 0.7596 (p0) cc_final: 0.7291 (p0) REVERT: U 107 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8456 (t0) REVERT: V 76 ASN cc_start: 0.7675 (p0) cc_final: 0.7113 (p0) REVERT: V 107 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (t0) REVERT: W 76 ASN cc_start: 0.7626 (p0) cc_final: 0.7319 (p0) REVERT: W 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8507 (t0) REVERT: X 76 ASN cc_start: 0.7653 (p0) cc_final: 0.7337 (p0) REVERT: X 107 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8479 (t0) outliers start: 34 outliers final: 10 residues processed: 399 average time/residue: 1.0775 time to fit residues: 542.5799 Evaluate side-chains 405 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP 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 F residue 111 ASP Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 111 ASP 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 J residue 111 ASP 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 O residue 111 ASP Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 111 ASP 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 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 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 334 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.149065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126426 restraints weight = 223672.439| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.64 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2070 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= 0.119 Angle : 0.409 5.609 45144 Z= 0.230 Chirality : 0.036 0.116 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.591 12.909 4320 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 11.37 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.13), residues: 3984 helix: 2.56 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.51 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 180 HIS 0.004 0.001 HIS O 39 PHE 0.010 0.001 PHE F 129 TYR 0.017 0.001 TYR D 24 ARG 0.003 0.001 ARG S 105 Details of bonding type rmsd hydrogen bonds : bond 0.06373 ( 2550) hydrogen bonds : angle 3.67231 ( 7626) covalent geometry : bond 0.00210 (33408) covalent geometry : angle 0.40908 (45144) ********************** 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 360 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 3.421 Fit side-chains REVERT: A 107 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8428 (t0) REVERT: B 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8419 (t0) REVERT: C 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (t0) REVERT: D 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t0) REVERT: E 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8425 (t0) REVERT: F 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8419 (t0) REVERT: G 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8397 (t0) REVERT: H 76 ASN cc_start: 0.7212 (p0) cc_final: 0.6733 (p0) REVERT: H 107 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8412 (t0) REVERT: I 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8433 (t0) REVERT: J 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8390 (t0) REVERT: K 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8402 (t0) REVERT: L 107 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8424 (t0) REVERT: M 107 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8400 (t0) REVERT: N 107 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8408 (t0) REVERT: O 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8409 (t0) REVERT: P 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8420 (t0) REVERT: Q 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (t0) REVERT: R 107 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8389 (t0) REVERT: S 107 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8406 (t0) REVERT: T 76 ASN cc_start: 0.7122 (p0) cc_final: 0.6646 (p0) REVERT: T 107 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8425 (t0) REVERT: U 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8384 (t0) REVERT: V 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8434 (t0) REVERT: W 107 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8421 (t0) REVERT: X 107 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8413 (t0) outliers start: 24 outliers final: 0 residues processed: 360 average time/residue: 0.9692 time to fit residues: 446.5314 Evaluate side-chains 359 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 3.659 ------------------------------------------------------------------------------- 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 168 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.141635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119451 restraints weight = 207210.664| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.38 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33408 Z= 0.173 Angle : 0.476 6.117 45144 Z= 0.264 Chirality : 0.038 0.125 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.756 13.489 4320 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.58 % Allowed : 11.88 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.13), residues: 3984 helix: 2.34 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.67 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 180 HIS 0.002 0.001 HIS K 39 PHE 0.011 0.001 PHE E 129 TYR 0.017 0.002 TYR I 24 ARG 0.003 0.001 ARG U 110 Details of bonding type rmsd hydrogen bonds : bond 0.08574 ( 2550) hydrogen bonds : angle 3.90093 ( 7626) covalent geometry : bond 0.00370 (33408) covalent geometry : angle 0.47646 (45144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14929.85 seconds wall clock time: 259 minutes 57.33 seconds (15597.33 seconds total)