Starting phenix.real_space_refine on Fri Jun 27 16:42:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqu_37754/06_2025/8wqu_37754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqu_37754/06_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_37754/06_2025/8wqu_37754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqu_37754/06_2025/8wqu_37754.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqu_37754/06_2025/8wqu_37754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqu_37754/06_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 30.88, 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: 7.70 Conformation dependent library (CDL) restraints added in 7.1 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: 3.02 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: 9.97 Time building geometry restraints manager: 9.10 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: 0.02 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: 0.770 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: 1.120 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 83.540 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.270 ------------------------------------------------------------------------------- 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 : 3.463 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: 1.2727 time to fit residues: 803.9647 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 : 3.816 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125687 restraints weight = 192050.903| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.28 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 7.416 Fit side-chains REVERT: A 114 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7682 (tttt) REVERT: B 114 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7689 (tttt) REVERT: C 114 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7686 (tttt) REVERT: D 114 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7669 (tttt) REVERT: E 114 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7689 (tttt) REVERT: F 114 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7694 (tttt) REVERT: G 114 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7668 (tttt) REVERT: H 114 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7683 (tttt) REVERT: I 114 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7681 (tttt) REVERT: J 114 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7683 (tttt) REVERT: K 114 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7669 (tttt) REVERT: L 114 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7696 (tttt) REVERT: M 114 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7702 (tttt) REVERT: N 114 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7684 (tttt) REVERT: O 114 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7695 (tttt) REVERT: P 114 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7684 (tttt) REVERT: Q 114 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7678 (tttt) REVERT: R 107 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (t0) REVERT: R 114 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7695 (tttt) REVERT: S 114 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7687 (tttt) REVERT: T 114 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7703 (tttt) REVERT: U 107 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8560 (t0) REVERT: U 114 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7677 (tttt) REVERT: V 114 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7685 (tttt) REVERT: W 114 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7702 (tttt) REVERT: X 114 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7701 (tttt) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 1.2768 time to fit residues: 679.8866 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 : 3.566 ------------------------------------------------------------------------------- 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: 2.9990 chunk 160 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 350 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.144891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122679 restraints weight = 199975.076| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.30 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33408 Z= 0.154 Angle : 0.460 5.469 45144 Z= 0.258 Chirality : 0.037 0.112 4896 Planarity : 0.003 0.039 5808 Dihedral : 3.851 11.978 4320 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.99 % Allowed : 8.61 % Favored : 90.40 % 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: 1.90 (0.13), residues: 3984 helix: 1.94 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.41 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 180 HIS 0.003 0.001 HIS K 39 PHE 0.011 0.001 PHE F 129 TYR 0.015 0.002 TYR D 24 ARG 0.004 0.001 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.08035 ( 2550) hydrogen bonds : angle 3.89190 ( 7626) covalent geometry : bond 0.00308 (33408) covalent geometry : angle 0.45969 (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 435 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 409 time to evaluate : 3.556 Fit side-chains REVERT: I 114 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7790 (tttt) REVERT: Q 114 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7790 (tttt) REVERT: R 107 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8504 (t0) REVERT: U 107 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8490 (t0) REVERT: W 114 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7824 (tttt) outliers start: 26 outliers final: 24 residues processed: 411 average time/residue: 1.2303 time to fit residues: 620.3573 Evaluate side-chains 382 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 356 time to evaluate : 4.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 132 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 335 optimal weight: 3.9990 chunk 322 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122137 restraints weight = 208596.232| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.33 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33408 Z= 0.156 Angle : 0.460 5.538 45144 Z= 0.257 Chirality : 0.037 0.115 4896 Planarity : 0.003 0.037 5808 Dihedral : 3.804 12.575 4320 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 8.59 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.19 (0.13), residues: 3984 helix: 2.12 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.21 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 180 HIS 0.003 0.001 HIS G 39 PHE 0.011 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 0.08088 ( 2550) hydrogen bonds : angle 3.85974 ( 7626) covalent geometry : bond 0.00314 (33408) covalent geometry : angle 0.46008 (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 446 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 373 time to evaluate : 4.235 Fit side-chains REVERT: B 107 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8539 (t0) REVERT: C 107 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8523 (t0) REVERT: F 107 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8540 (t0) REVERT: O 107 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8522 (t0) REVERT: P 107 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8528 (t0) REVERT: R 107 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8525 (t0) REVERT: T 107 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8536 (t0) REVERT: U 107 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8499 (t0) REVERT: X 107 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8532 (t0) outliers start: 73 outliers final: 24 residues processed: 404 average time/residue: 1.2506 time to fit residues: 625.0829 Evaluate side-chains 402 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 369 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP 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 111 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 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 111 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 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 111 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 107 ASN Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 122 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 86 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 339 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 332 optimal weight: 3.9990 overall best weight: 1.4240 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.148178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125776 restraints weight = 206630.300| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.45 r_work (final): 0.3487 ------------------------------------------------------------------------------- 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 = 0.34 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1880 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 : 0.420 5.463 45144 Z= 0.235 Chirality : 0.036 0.114 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.652 12.632 4320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.91 % Allowed : 9.83 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.45 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.87 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 180 HIS 0.005 0.001 HIS Q 39 PHE 0.009 0.001 PHE F 129 TYR 0.015 0.001 TYR D 24 ARG 0.003 0.000 ARG T 110 Details of bonding type rmsd hydrogen bonds : bond 0.06765 ( 2550) hydrogen bonds : angle 3.70217 ( 7626) covalent geometry : bond 0.00233 (33408) covalent geometry : angle 0.41998 (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 407 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 3.962 Fit side-chains REVERT: A 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (t0) REVERT: B 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8450 (t0) REVERT: C 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8422 (t0) REVERT: D 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8445 (t0) REVERT: E 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8461 (t0) REVERT: F 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8433 (t0) REVERT: G 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8415 (t0) REVERT: H 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8441 (t0) REVERT: I 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8469 (t0) REVERT: J 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8415 (t0) REVERT: K 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8442 (t0) REVERT: L 107 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8446 (t0) REVERT: M 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8439 (t0) REVERT: N 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8457 (t0) REVERT: O 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (t0) REVERT: P 107 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8450 (t0) REVERT: Q 107 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8469 (t0) REVERT: R 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8425 (t0) REVERT: S 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8444 (t0) REVERT: T 107 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8449 (t0) REVERT: U 107 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8424 (t0) REVERT: V 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8468 (t0) REVERT: W 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (t0) REVERT: X 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8419 (t0) outliers start: 48 outliers final: 0 residues processed: 383 average time/residue: 1.0036 time to fit residues: 493.3695 Evaluate side-chains 386 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 362 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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=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: 7.9990 chunk 357 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 361 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 343 optimal weight: 0.0030 overall best weight: 3.1996 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.141328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118756 restraints weight = 216565.439| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.38 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 33408 Z= 0.189 Angle : 0.499 5.808 45144 Z= 0.277 Chirality : 0.039 0.127 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.857 13.259 4320 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.00 % Allowed : 10.33 % 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: 2.37 (0.13), residues: 3984 helix: 2.20 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.91 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 180 HIS 0.003 0.001 HIS D 39 PHE 0.011 0.002 PHE F 129 TYR 0.017 0.002 TYR Q 24 ARG 0.004 0.000 ARG F 110 Details of bonding type rmsd hydrogen bonds : bond 0.09205 ( 2550) hydrogen bonds : angle 3.97077 ( 7626) covalent geometry : bond 0.00410 (33408) covalent geometry : angle 0.49924 (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 423 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 375 time to evaluate : 3.991 Fit side-chains REVERT: A 107 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8567 (t0) REVERT: B 76 ASN cc_start: 0.7720 (p0) cc_final: 0.7406 (p0) REVERT: B 107 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8549 (t0) REVERT: C 107 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8531 (t0) REVERT: D 107 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8550 (t0) REVERT: E 107 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8538 (t0) REVERT: F 76 ASN cc_start: 0.7736 (p0) cc_final: 0.7395 (p0) REVERT: F 107 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8547 (t0) REVERT: G 76 ASN cc_start: 0.7753 (p0) cc_final: 0.7419 (p0) REVERT: G 107 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8529 (t0) REVERT: I 76 ASN cc_start: 0.7733 (p0) cc_final: 0.7387 (p0) REVERT: I 107 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8574 (t0) REVERT: J 107 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8516 (t0) REVERT: L 107 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8546 (t0) REVERT: M 107 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8542 (t0) REVERT: N 107 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8559 (t0) REVERT: O 107 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8525 (t0) REVERT: P 107 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8533 (t0) REVERT: Q 107 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8568 (t0) REVERT: R 107 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8548 (t0) REVERT: T 107 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8545 (t0) REVERT: U 107 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8509 (t0) REVERT: V 107 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8549 (t0) REVERT: W 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8562 (t0) REVERT: X 76 ASN cc_start: 0.7762 (p0) cc_final: 0.7421 (p0) REVERT: X 107 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8546 (t0) outliers start: 48 outliers final: 0 residues processed: 399 average time/residue: 1.0948 time to fit residues: 546.7313 Evaluate side-chains 376 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 355 time to evaluate : 3.580 ------------------------------------------------------------------------------- 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 I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 207 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 303 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.150747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128548 restraints weight = 191738.182| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.35 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2091 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= 0.115 Angle : 0.406 5.653 45144 Z= 0.226 Chirality : 0.036 0.114 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.577 12.599 4320 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 10.64 % Favored : 87.84 % 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: 2.98 (0.13), residues: 3984 helix: 2.60 (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 0.000 TRP A 180 HIS 0.005 0.001 HIS I 39 PHE 0.008 0.001 PHE F 129 TYR 0.016 0.001 TYR D 24 ARG 0.003 0.000 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 2550) hydrogen bonds : angle 3.61821 ( 7626) covalent geometry : bond 0.00203 (33408) covalent geometry : angle 0.40566 (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 390 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 360 time to evaluate : 3.906 Fit side-chains REVERT: A 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 107 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (t0) REVERT: C 107 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8458 (t0) REVERT: D 107 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (t0) REVERT: E 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8451 (t0) REVERT: F 107 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8463 (t0) REVERT: G 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8440 (t0) REVERT: H 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8434 (t0) REVERT: I 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8455 (t0) REVERT: J 107 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8445 (t0) REVERT: K 107 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (t0) REVERT: L 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8427 (t0) REVERT: M 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8414 (t0) REVERT: N 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8427 (t0) REVERT: O 107 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8470 (t0) REVERT: P 107 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8485 (t0) REVERT: Q 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8441 (t0) REVERT: R 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8413 (t0) REVERT: S 107 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8435 (t0) REVERT: T 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8460 (t0) REVERT: U 107 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8453 (t0) REVERT: V 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8459 (t0) REVERT: W 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8429 (t0) REVERT: X 107 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8467 (t0) outliers start: 30 outliers final: 0 residues processed: 384 average time/residue: 1.0691 time to fit residues: 513.8251 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 : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 188 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 327 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.152267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130023 restraints weight = 206309.850| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.40 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2295 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= 0.110 Angle : 0.391 5.653 45144 Z= 0.220 Chirality : 0.036 0.122 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.486 12.600 4320 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.44 % Allowed : 11.99 % Favored : 86.57 % 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: 3.07 (0.13), residues: 3984 helix: 2.66 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.50 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 PHE 0.008 0.001 PHE F 129 TYR 0.015 0.001 TYR D 24 ARG 0.003 0.000 ARG T 110 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 2550) hydrogen bonds : angle 3.59498 ( 7626) covalent geometry : bond 0.00192 (33408) covalent geometry : angle 0.39139 (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 371 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 3.439 Fit side-chains REVERT: A 107 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8540 (t0) REVERT: B 107 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8525 (t0) REVERT: C 107 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8516 (t0) REVERT: D 107 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8516 (t0) REVERT: E 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8549 (t0) REVERT: F 107 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8519 (t0) REVERT: G 107 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8523 (t0) REVERT: H 107 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8541 (t0) REVERT: I 107 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8542 (t0) REVERT: J 107 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8503 (t0) REVERT: K 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (t0) REVERT: L 107 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8536 (t0) REVERT: M 107 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8537 (t0) REVERT: N 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8511 (t0) REVERT: O 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8524 (t0) REVERT: P 107 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8528 (t0) REVERT: R 107 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8529 (t0) REVERT: S 107 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8523 (t0) REVERT: T 107 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8469 (m-40) REVERT: U 107 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (t0) REVERT: V 107 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8557 (t0) REVERT: W 107 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8536 (t0) REVERT: X 107 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8520 (t0) outliers start: 27 outliers final: 0 residues processed: 367 average time/residue: 0.9681 time to fit residues: 453.2637 Evaluate side-chains 359 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 336 time to evaluate : 3.669 ------------------------------------------------------------------------------- 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 R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 0.8980 chunk 335 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 285 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.150793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128336 restraints weight = 207410.723| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.51 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2260 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= 0.115 Angle : 0.401 6.035 45144 Z= 0.224 Chirality : 0.036 0.123 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.475 12.661 4320 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.58 % Allowed : 12.70 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.12 (0.13), residues: 3984 helix: 2.68 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.44 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 PHE 0.008 0.001 PHE F 129 TYR 0.014 0.001 TYR N 24 ARG 0.003 0.000 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.06072 ( 2550) hydrogen bonds : angle 3.60482 ( 7626) covalent geometry : bond 0.00207 (33408) covalent geometry : angle 0.40073 (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 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 3.741 Fit side-chains REVERT: A 107 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (t0) REVERT: B 107 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8450 (t0) REVERT: C 107 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (t0) REVERT: D 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8453 (t0) REVERT: E 107 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8478 (t0) REVERT: F 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8448 (t0) REVERT: G 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8444 (t0) REVERT: H 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8473 (t0) REVERT: I 107 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8470 (t0) REVERT: J 107 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8422 (t0) REVERT: K 107 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (t0) REVERT: L 107 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8465 (t0) REVERT: M 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (t0) REVERT: N 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8452 (t0) REVERT: O 107 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (t0) REVERT: P 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8457 (t0) REVERT: Q 107 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (t0) REVERT: R 107 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8464 (t0) REVERT: S 107 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8443 (t0) REVERT: T 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8462 (t0) REVERT: U 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (t0) REVERT: V 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8474 (t0) REVERT: W 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8460 (t0) REVERT: X 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8448 (t0) outliers start: 32 outliers final: 0 residues processed: 366 average time/residue: 1.1522 time to fit residues: 546.3178 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 : 4.012 ------------------------------------------------------------------------------- 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 334 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 207 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.145261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122876 restraints weight = 224593.918| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.54 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1913 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= 0.145 Angle : 0.440 6.064 45144 Z= 0.245 Chirality : 0.037 0.127 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.612 13.215 4320 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.35 % Allowed : 13.15 % Favored : 85.50 % 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: 2.89 (0.13), residues: 3984 helix: 2.53 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.55 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 180 HIS 0.004 0.001 HIS K 39 PHE 0.010 0.001 PHE O 129 TYR 0.016 0.002 TYR I 24 ARG 0.003 0.000 ARG T 110 Details of bonding type rmsd hydrogen bonds : bond 0.07551 ( 2550) hydrogen bonds : angle 3.78544 ( 7626) covalent geometry : bond 0.00289 (33408) covalent geometry : angle 0.43951 (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 384 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 360 time to evaluate : 3.523 Fit side-chains REVERT: A 107 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (t0) REVERT: B 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8450 (t0) REVERT: C 107 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (t0) REVERT: D 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8460 (t0) REVERT: E 107 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8461 (t0) REVERT: F 107 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (t0) REVERT: G 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8435 (t0) REVERT: H 107 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (t0) REVERT: I 107 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8485 (t0) REVERT: J 107 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8450 (t0) REVERT: K 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8451 (t0) REVERT: L 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (t0) REVERT: M 107 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8456 (t0) REVERT: N 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8466 (t0) REVERT: O 107 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8445 (t0) REVERT: P 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8448 (t0) REVERT: Q 107 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (t0) REVERT: R 107 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (t0) REVERT: S 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8456 (t0) REVERT: T 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8448 (t0) REVERT: U 107 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8430 (t0) REVERT: V 107 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8466 (t0) REVERT: W 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8462 (t0) REVERT: X 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8447 (t0) outliers start: 24 outliers final: 0 residues processed: 384 average time/residue: 0.9536 time to fit residues: 467.6601 Evaluate side-chains 384 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 360 time to evaluate : 3.749 ------------------------------------------------------------------------------- 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: 5.9990 chunk 283 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118308 restraints weight = 207145.244| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.27 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1530 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= 0.195 Angle : 0.507 6.051 45144 Z= 0.279 Chirality : 0.040 0.131 4896 Planarity : 0.003 0.034 5808 Dihedral : 3.831 13.646 4320 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.35 % Allowed : 13.20 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.52 (0.13), residues: 3984 helix: 2.27 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.70 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P 180 HIS 0.003 0.001 HIS Q 112 PHE 0.011 0.002 PHE E 129 TYR 0.017 0.002 TYR I 24 ARG 0.004 0.000 ARG U 110 Details of bonding type rmsd hydrogen bonds : bond 0.09376 ( 2550) hydrogen bonds : angle 4.02032 ( 7626) covalent geometry : bond 0.00430 (33408) covalent geometry : angle 0.50709 (45144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16392.19 seconds wall clock time: 287 minutes 30.80 seconds (17250.80 seconds total)