Starting phenix.real_space_refine on Wed Mar 4 15:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxa_35074/03_2026/8hxa_35074.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 9336 2.51 5 N 2466 2.21 5 O 2862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14790 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "B" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "C" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "D" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "F" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "G" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "H" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "I" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "J" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 855 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Time building chain proxies: 3.26, per 1000 atoms: 0.22 Number of scatterers: 14790 At special positions: 0 Unit cell: (170.05, 162.45, 65.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 2862 8.00 N 2466 7.00 C 9336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 130 " distance=2.07 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS F 25 " distance=2.04 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=1.93 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS D 130 " distance=2.06 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.04 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.05 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 50 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 116 " distance=2.03 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 116 " distance=2.03 Simple disulfide: pdb=" SG CYS K 50 " - pdb=" SG CYS K 116 " distance=2.03 Simple disulfide: pdb=" SG CYS L 50 " - pdb=" SG CYS L 116 " distance=2.03 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: 1.08 Conformation dependent library (CDL) restraints added in 622.6 milliseconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 30 sheets defined 5.2% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG A 191 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG B 191 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG C 191 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG E 191 " --> pdb=" O TYR E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.510A pdb=" N ARG F 191 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 removed outlier: 4.152A pdb=" N ALA G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'H' and resid 55 through 60 removed outlier: 4.153A pdb=" N ALA H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'I' and resid 55 through 60 removed outlier: 4.153A pdb=" N ALA I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.153A pdb=" N ALA J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 111 Processing helix chain 'K' and resid 55 through 60 removed outlier: 4.152A pdb=" N ALA K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 111 Processing helix chain 'L' and resid 55 through 60 removed outlier: 4.153A pdb=" N ALA L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 7.458A pdb=" N VAL A 37 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 165 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A 39 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 163 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 41 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 161 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY A 43 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N SER A 193 " --> pdb=" O HIS G 130 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N HIS G 130 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 195 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE G 36 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER G 137 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL G 38 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS G 139 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS G 40 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.758A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 37 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 165 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A 39 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 163 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 41 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 161 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY A 43 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N SER A 193 " --> pdb=" O HIS G 130 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N HIS G 130 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 195 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL G 118 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 131 " --> pdb=" O CYS G 116 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS G 116 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU G 133 " --> pdb=" O TYR G 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR G 114 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR G 135 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY G 112 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS G 68 " --> pdb=" O MET G 72 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE A 119 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR A 152 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 121 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN A 154 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 123 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 132 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE A 119 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR A 152 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 121 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN A 154 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 123 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 184 removed outlier: 7.458A pdb=" N VAL B 37 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 165 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B 39 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 163 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR B 41 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 161 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY B 43 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N SER B 193 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS L 130 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY B 195 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE L 36 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER L 137 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL L 38 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS L 139 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS L 40 " --> pdb=" O LYS L 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216 removed outlier: 3.760A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 37 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 165 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B 39 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 163 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR B 41 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 161 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY B 43 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N SER B 193 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS L 130 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY B 195 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL L 118 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 131 " --> pdb=" O CYS L 116 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS L 116 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU L 133 " --> pdb=" O TYR L 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR L 114 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR L 135 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY L 112 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS L 68 " --> pdb=" O MET L 72 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET L 72 " --> pdb=" O LYS L 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE B 119 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR B 152 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 121 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN B 154 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 123 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 132 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE B 119 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR B 152 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 121 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN B 154 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 123 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 184 removed outlier: 7.459A pdb=" N VAL C 37 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 165 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU C 39 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 163 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 41 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 161 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY C 43 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N SER C 193 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N HIS K 130 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY C 195 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE K 36 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER K 137 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL K 38 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS K 139 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS K 40 " --> pdb=" O LYS K 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.759A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL C 37 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 165 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU C 39 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 163 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 41 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 161 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY C 43 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N SER C 193 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N HIS K 130 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY C 195 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL K 118 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU K 131 " --> pdb=" O CYS K 116 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS K 116 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU K 133 " --> pdb=" O TYR K 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR K 114 " --> pdb=" O GLU K 133 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR K 135 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY K 112 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS K 68 " --> pdb=" O MET K 72 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 62 removed outlier: 7.247A pdb=" N ILE C 119 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 152 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 121 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN C 154 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 123 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 132 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 62 removed outlier: 7.247A pdb=" N ILE C 119 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 152 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 121 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN C 154 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 123 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 181 through 184 removed outlier: 7.457A pdb=" N VAL D 37 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR D 165 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU D 39 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 163 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 41 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 161 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY D 43 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N SER D 193 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS J 130 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY D 195 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE J 36 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER J 137 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL J 38 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LYS J 139 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS J 40 " --> pdb=" O LYS J 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 215 through 216 removed outlier: 3.759A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL D 37 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR D 165 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU D 39 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 163 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 41 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 161 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY D 43 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N SER D 193 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS J 130 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY D 195 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL J 118 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU J 131 " --> pdb=" O CYS J 116 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS J 116 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU J 133 " --> pdb=" O TYR J 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR J 114 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR J 135 " --> pdb=" O GLY J 112 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY J 112 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS J 68 " --> pdb=" O MET J 72 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE D 119 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR D 152 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 121 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN D 154 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 123 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 132 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE D 119 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR D 152 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 121 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN D 154 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 123 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 181 through 184 removed outlier: 7.457A pdb=" N VAL E 37 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR E 165 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU E 39 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 163 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 41 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL E 161 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY E 43 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N SER E 193 " --> pdb=" O HIS I 130 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS I 130 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY E 195 " --> pdb=" O ARG I 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE I 36 " --> pdb=" O THR I 135 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER I 137 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL I 38 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LYS I 139 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS I 40 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 215 through 216 removed outlier: 3.759A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL E 37 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR E 165 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU E 39 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 163 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 41 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL E 161 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY E 43 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N SER E 193 " --> pdb=" O HIS I 130 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS I 130 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY E 195 " --> pdb=" O ARG I 128 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL I 118 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 131 " --> pdb=" O CYS I 116 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS I 116 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU I 133 " --> pdb=" O TYR I 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR I 114 " --> pdb=" O GLU I 133 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR I 135 " --> pdb=" O GLY I 112 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY I 112 " --> pdb=" O THR I 135 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS I 68 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE E 119 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR E 152 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 121 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN E 154 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE E 123 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR E 132 " --> pdb=" O GLY E 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE E 119 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR E 152 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 121 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN E 154 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE E 123 " --> pdb=" O ASN E 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 181 through 184 removed outlier: 7.458A pdb=" N VAL F 37 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR F 165 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU F 39 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU F 163 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR F 41 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL F 161 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY F 43 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N SER F 193 " --> pdb=" O HIS H 130 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS H 130 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY F 195 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE H 36 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER H 137 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL H 38 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS H 139 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS H 40 " --> pdb=" O LYS H 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 215 through 216 removed outlier: 3.759A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL F 37 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR F 165 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU F 39 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU F 163 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR F 41 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL F 161 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY F 43 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N SER F 193 " --> pdb=" O HIS H 130 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS H 130 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY F 195 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL H 118 " --> pdb=" O GLU H 129 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 131 " --> pdb=" O CYS H 116 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS H 116 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU H 133 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR H 114 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR H 135 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY H 112 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS H 68 " --> pdb=" O MET H 72 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N MET H 72 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE F 119 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR F 152 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL F 121 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN F 154 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE F 123 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR F 132 " --> pdb=" O GLY F 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 57 through 62 removed outlier: 7.246A pdb=" N ILE F 119 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR F 152 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL F 121 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN F 154 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE F 123 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AC8, first strand: chain 'H' and resid 46 through 48 Processing sheet with id=AC9, first strand: chain 'I' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'J' and resid 46 through 48 Processing sheet with id=AD2, first strand: chain 'K' and resid 46 through 48 Processing sheet with id=AD3, first strand: chain 'L' and resid 46 through 48 660 hydrogen bonds defined for protein. 1656 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: 2.38 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3162 1.33 - 1.45: 3346 1.45 - 1.57: 8373 1.57 - 1.69: 5 1.69 - 1.82: 186 Bond restraints: 15072 Sorted by residual: bond pdb=" N TYR A 218 " pdb=" CA TYR A 218 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.16e-02 7.43e+03 8.19e+00 bond pdb=" N TYR E 218 " pdb=" CA TYR E 218 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 8.16e+00 bond pdb=" N TYR D 218 " pdb=" CA TYR D 218 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.66e+00 bond pdb=" CB ASP E 64 " pdb=" CG ASP E 64 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.18e+00 bond pdb=" N LYS C 169 " pdb=" CA LYS C 169 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.22e-02 6.72e+03 5.17e+00 ... (remaining 15067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 20012 3.01 - 6.02: 305 6.02 - 9.03: 67 9.03 - 12.04: 22 12.04 - 15.05: 12 Bond angle restraints: 20418 Sorted by residual: angle pdb=" C TYR F 218 " pdb=" N ARG F 219 " pdb=" CA ARG F 219 " ideal model delta sigma weight residual 122.35 130.08 -7.73 1.46e+00 4.69e-01 2.81e+01 angle pdb=" C TYR C 218 " pdb=" N ARG C 219 " pdb=" CA ARG C 219 " ideal model delta sigma weight residual 122.35 129.67 -7.32 1.46e+00 4.69e-01 2.51e+01 angle pdb=" CB ARG F 219 " pdb=" CG ARG F 219 " pdb=" CD ARG F 219 " ideal model delta sigma weight residual 111.30 100.33 10.97 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C TYR B 218 " pdb=" N ARG B 219 " pdb=" CA ARG B 219 " ideal model delta sigma weight residual 122.36 129.03 -6.67 1.47e+00 4.63e-01 2.06e+01 angle pdb=" CB ARG C 219 " pdb=" CG ARG C 219 " pdb=" CD ARG C 219 " ideal model delta sigma weight residual 111.30 101.21 10.09 2.30e+00 1.89e-01 1.93e+01 ... (remaining 20413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 7773 16.36 - 32.72: 1097 32.72 - 49.08: 271 49.08 - 65.45: 45 65.45 - 81.81: 18 Dihedral angle restraints: 9204 sinusoidal: 3732 harmonic: 5472 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 173.93 -80.93 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS C 160 " pdb=" SG CYS C 160 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 173.90 -80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 160 " pdb=" SG CYS B 160 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual 93.00 173.89 -80.89 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1512 0.049 - 0.097: 553 0.097 - 0.146: 256 0.146 - 0.194: 11 0.194 - 0.243: 14 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CB ILE B 209 " pdb=" CA ILE B 209 " pdb=" CG1 ILE B 209 " pdb=" CG2 ILE B 209 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE E 209 " pdb=" CA ILE E 209 " pdb=" CG1 ILE E 209 " pdb=" CG2 ILE E 209 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE F 209 " pdb=" CA ILE F 209 " pdb=" CG1 ILE F 209 " pdb=" CG2 ILE F 209 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2343 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 64 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C ASP A 64 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 64 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 65 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 64 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ASP F 64 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP F 64 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG F 65 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 64 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ASP B 64 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP B 64 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 65 " 0.020 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 126 2.60 - 3.17: 11519 3.17 - 3.75: 22465 3.75 - 4.32: 33062 4.32 - 4.90: 54918 Nonbonded interactions: 122090 Sorted by model distance: nonbonded pdb=" OE2 GLU D 60 " pdb=" O GLU D 220 " model vdw 2.023 3.040 nonbonded pdb=" OE2 GLU E 60 " pdb=" O GLU E 220 " model vdw 2.062 3.040 nonbonded pdb=" OE2 GLU A 60 " pdb=" O GLU A 220 " model vdw 2.111 3.040 nonbonded pdb=" NH2 ARG B 32 " pdb=" OE2 GLU C 127 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG D 32 " pdb=" OE2 GLU E 127 " model vdw 2.309 3.120 ... (remaining 122085 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=0.93 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: 2.060 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 15102 Z= 0.230 Angle : 1.067 15.052 20478 Z= 0.530 Chirality : 0.059 0.243 2346 Planarity : 0.006 0.037 2568 Dihedral : 15.671 81.808 5586 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.12 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 22.61 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1818 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 810 loop : -0.99 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG I 128 TYR 0.020 0.002 TYR B 218 PHE 0.009 0.002 PHE F 198 TRP 0.019 0.003 TRP H 66 HIS 0.008 0.002 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00460 (15072) covalent geometry : angle 1.06072 (20418) SS BOND : bond 0.02167 ( 30) SS BOND : angle 2.39525 ( 60) hydrogen bonds : bond 0.20793 ( 480) hydrogen bonds : angle 8.20109 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.555 Fit side-chains REVERT: A 189 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8679 (t) REVERT: B 32 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7709 (mtm-85) REVERT: B 80 MET cc_start: 0.8503 (ttt) cc_final: 0.8209 (ttt) REVERT: B 169 LYS cc_start: 0.8214 (ptpp) cc_final: 0.8001 (ptpp) REVERT: C 21 LYS cc_start: 0.7634 (ptmm) cc_final: 0.7214 (pptt) REVERT: C 31 TYR cc_start: 0.8484 (m-80) cc_final: 0.8172 (m-80) REVERT: C 58 MET cc_start: 0.9105 (ptm) cc_final: 0.8898 (ptm) REVERT: C 178 LYS cc_start: 0.6925 (mmtm) cc_final: 0.6724 (mmtt) REVERT: E 32 ARG cc_start: 0.8366 (mtm180) cc_final: 0.8049 (mtm-85) REVERT: E 80 MET cc_start: 0.8578 (ttt) cc_final: 0.8340 (ttt) REVERT: F 164 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8161 (mm-30) REVERT: F 178 LYS cc_start: 0.7129 (mmtm) cc_final: 0.6914 (mmtt) REVERT: F 197 THR cc_start: 0.9145 (t) cc_final: 0.8521 (p) REVERT: K 76 MET cc_start: 0.7982 (tpp) cc_final: 0.7653 (ttp) REVERT: L 120 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7849 (ttpp) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.1417 time to fit residues: 45.5092 Evaluate side-chains 222 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.183800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120178 restraints weight = 15622.810| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.96 r_work: 0.3159 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15102 Z= 0.187 Angle : 0.704 11.363 20478 Z= 0.351 Chirality : 0.051 0.132 2346 Planarity : 0.003 0.028 2568 Dihedral : 4.589 17.770 2011 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.47 % Favored : 96.20 % Rotamer: Outliers : 3.36 % Allowed : 20.67 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 822 loop : -0.79 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 219 TYR 0.016 0.002 TYR G 65 PHE 0.007 0.001 PHE B 198 TRP 0.007 0.001 TRP B 34 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00436 (15072) covalent geometry : angle 0.69750 (20418) SS BOND : bond 0.00356 ( 30) SS BOND : angle 1.95031 ( 60) hydrogen bonds : bond 0.04040 ( 480) hydrogen bonds : angle 5.84039 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.502 Fit side-chains REVERT: A 32 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8467 (mtp180) REVERT: A 197 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 32 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8365 (mtp180) REVERT: B 86 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: C 152 THR cc_start: 0.8933 (t) cc_final: 0.8332 (p) REVERT: D 32 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8469 (mtp180) REVERT: D 197 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8408 (p) REVERT: E 32 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8349 (mtp180) REVERT: E 152 THR cc_start: 0.8907 (t) cc_final: 0.8341 (p) REVERT: F 152 THR cc_start: 0.8929 (t) cc_final: 0.8349 (p) REVERT: F 197 THR cc_start: 0.9001 (t) cc_final: 0.8601 (p) REVERT: J 81 MET cc_start: 0.7842 (tmm) cc_final: 0.7495 (ttm) REVERT: J 101 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6088 (pt) REVERT: K 76 MET cc_start: 0.7033 (tpp) cc_final: 0.6791 (ttp) REVERT: K 101 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6211 (pt) REVERT: L 120 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7202 (ttpp) outliers start: 57 outliers final: 37 residues processed: 265 average time/residue: 0.1473 time to fit residues: 55.3980 Evaluate side-chains 249 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 138 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 168 optimal weight: 0.0070 chunk 43 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.186843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122984 restraints weight = 15812.787| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.09 r_work: 0.3175 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15102 Z= 0.106 Angle : 0.590 11.224 20478 Z= 0.295 Chirality : 0.048 0.133 2346 Planarity : 0.003 0.023 2568 Dihedral : 4.259 15.433 2010 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 20.49 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.15 (0.18), residues: 822 loop : -0.69 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.012 0.001 TYR K 121 PHE 0.005 0.001 PHE C 198 TRP 0.008 0.001 TRP J 66 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00230 (15072) covalent geometry : angle 0.58839 (20418) SS BOND : bond 0.00153 ( 30) SS BOND : angle 1.02615 ( 60) hydrogen bonds : bond 0.02980 ( 480) hydrogen bonds : angle 5.31288 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8492 (mtp180) REVERT: A 197 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 32 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8420 (mtp180) REVERT: B 86 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: C 64 ASP cc_start: 0.7805 (t0) cc_final: 0.7514 (t0) REVERT: D 32 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8468 (mtp180) REVERT: D 64 ASP cc_start: 0.7699 (t0) cc_final: 0.7486 (t0) REVERT: D 197 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8324 (p) REVERT: E 32 ARG cc_start: 0.8668 (mtm180) cc_final: 0.8413 (mtp180) REVERT: E 64 ASP cc_start: 0.7850 (t0) cc_final: 0.7524 (t0) REVERT: E 150 ASP cc_start: 0.8501 (t70) cc_final: 0.8144 (t70) REVERT: E 206 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6587 (pp) REVERT: F 206 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7357 (mt) REVERT: J 76 MET cc_start: 0.7453 (ttt) cc_final: 0.7147 (ttp) REVERT: K 120 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7000 (ttpp) REVERT: L 120 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7044 (ttpp) outliers start: 52 outliers final: 28 residues processed: 279 average time/residue: 0.1472 time to fit residues: 57.3223 Evaluate side-chains 243 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.177983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129231 restraints weight = 15732.497| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.60 r_work: 0.3083 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15102 Z= 0.251 Angle : 0.689 10.334 20478 Z= 0.347 Chirality : 0.052 0.142 2346 Planarity : 0.004 0.029 2568 Dihedral : 4.390 16.884 2010 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 5.24 % Allowed : 18.90 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.03 (0.17), residues: 852 loop : -0.45 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 219 TYR 0.017 0.002 TYR G 65 PHE 0.008 0.002 PHE B 198 TRP 0.004 0.001 TRP I 66 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00604 (15072) covalent geometry : angle 0.68447 (20418) SS BOND : bond 0.00477 ( 30) SS BOND : angle 1.62707 ( 60) hydrogen bonds : bond 0.03404 ( 480) hydrogen bonds : angle 5.25936 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 205 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7934 (t0) cc_final: 0.7658 (t0) REVERT: B 32 ARG cc_start: 0.8788 (mtm180) cc_final: 0.8524 (mtp180) REVERT: B 64 ASP cc_start: 0.7905 (t0) cc_final: 0.7628 (t0) REVERT: C 64 ASP cc_start: 0.7989 (t0) cc_final: 0.7673 (t0) REVERT: C 152 THR cc_start: 0.8954 (t) cc_final: 0.8165 (p) REVERT: E 32 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8566 (mtp180) REVERT: E 64 ASP cc_start: 0.8055 (t0) cc_final: 0.7760 (t0) REVERT: E 152 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 206 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.6994 (pp) REVERT: F 64 ASP cc_start: 0.7968 (t0) cc_final: 0.7678 (t0) REVERT: F 152 THR cc_start: 0.9018 (t) cc_final: 0.8244 (p) REVERT: J 76 MET cc_start: 0.7677 (ttt) cc_final: 0.7150 (ttp) REVERT: J 96 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7653 (t) REVERT: K 76 MET cc_start: 0.7726 (ttp) cc_final: 0.7416 (ttt) REVERT: L 120 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7331 (ttpp) outliers start: 89 outliers final: 64 residues processed: 279 average time/residue: 0.1301 time to fit residues: 53.0231 Evaluate side-chains 263 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 79 ASN C 68 ASN C 79 ASN E 68 ASN E 79 ASN F 68 ASN F 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.181008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132605 restraints weight = 15826.898| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.54 r_work: 0.3127 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15102 Z= 0.129 Angle : 0.583 8.041 20478 Z= 0.297 Chirality : 0.048 0.139 2346 Planarity : 0.003 0.024 2568 Dihedral : 4.213 16.608 2010 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.51 % Favored : 95.16 % Rotamer: Outliers : 3.89 % Allowed : 22.14 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.01 (0.17), residues: 852 loop : -0.42 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 219 TYR 0.012 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.007 0.001 TRP I 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00301 (15072) covalent geometry : angle 0.58016 (20418) SS BOND : bond 0.00214 ( 30) SS BOND : angle 1.27250 ( 60) hydrogen bonds : bond 0.02717 ( 480) hydrogen bonds : angle 4.98544 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 196 time to evaluate : 0.586 Fit side-chains REVERT: A 64 ASP cc_start: 0.7936 (t0) cc_final: 0.7668 (t0) REVERT: B 64 ASP cc_start: 0.7922 (t0) cc_final: 0.7638 (t0) REVERT: B 189 SER cc_start: 0.9112 (m) cc_final: 0.8902 (t) REVERT: C 64 ASP cc_start: 0.7962 (t0) cc_final: 0.7622 (t0) REVERT: C 152 THR cc_start: 0.8978 (t) cc_final: 0.8176 (p) REVERT: E 64 ASP cc_start: 0.8059 (t0) cc_final: 0.7764 (t0) REVERT: E 98 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7783 (mttm) REVERT: E 152 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8274 (p) REVERT: E 206 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6934 (pp) REVERT: F 64 ASP cc_start: 0.8002 (t0) cc_final: 0.7686 (t0) REVERT: I 76 MET cc_start: 0.7912 (ttt) cc_final: 0.7460 (ttp) REVERT: J 76 MET cc_start: 0.7696 (ttt) cc_final: 0.7207 (ttp) REVERT: K 76 MET cc_start: 0.7850 (ttp) cc_final: 0.7453 (ttt) REVERT: L 120 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7296 (ttpp) outliers start: 66 outliers final: 47 residues processed: 251 average time/residue: 0.1390 time to fit residues: 49.9722 Evaluate side-chains 234 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 0.0040 chunk 100 optimal weight: 0.9980 chunk 132 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 79 ASN C 79 ASN E 79 ASN F 79 ASN K 37 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131517 restraints weight = 15749.127| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.47 r_work: 0.3198 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15102 Z= 0.144 Angle : 0.579 8.576 20478 Z= 0.294 Chirality : 0.048 0.140 2346 Planarity : 0.003 0.030 2568 Dihedral : 4.155 16.678 2010 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 4.36 % Allowed : 22.32 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.02 (0.18), residues: 852 loop : -0.41 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 219 TYR 0.013 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.006 0.001 TRP I 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00339 (15072) covalent geometry : angle 0.57548 (20418) SS BOND : bond 0.00252 ( 30) SS BOND : angle 1.26005 ( 60) hydrogen bonds : bond 0.02644 ( 480) hydrogen bonds : angle 4.93570 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 0.577 Fit side-chains REVERT: A 64 ASP cc_start: 0.7997 (t0) cc_final: 0.7762 (t0) REVERT: B 64 ASP cc_start: 0.8008 (t0) cc_final: 0.7716 (t0) REVERT: C 64 ASP cc_start: 0.8039 (t0) cc_final: 0.7714 (t0) REVERT: C 152 THR cc_start: 0.8979 (t) cc_final: 0.8169 (p) REVERT: E 64 ASP cc_start: 0.8124 (t0) cc_final: 0.7887 (t0) REVERT: E 98 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7884 (mttm) REVERT: E 152 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8261 (p) REVERT: E 206 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.6997 (pp) REVERT: F 64 ASP cc_start: 0.8076 (t0) cc_final: 0.7781 (t0) REVERT: I 76 MET cc_start: 0.7940 (ttt) cc_final: 0.7497 (ttp) REVERT: J 76 MET cc_start: 0.7749 (ttt) cc_final: 0.7265 (ttp) REVERT: K 76 MET cc_start: 0.7939 (ttp) cc_final: 0.7508 (ttt) REVERT: K 96 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7885 (t) REVERT: L 120 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7535 (ttpp) outliers start: 74 outliers final: 56 residues processed: 241 average time/residue: 0.1356 time to fit residues: 47.2749 Evaluate side-chains 240 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131298 restraints weight = 15614.631| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.59 r_work: 0.3151 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15102 Z= 0.133 Angle : 0.569 8.849 20478 Z= 0.290 Chirality : 0.048 0.140 2346 Planarity : 0.003 0.030 2568 Dihedral : 4.118 16.649 2010 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 3.47 % Allowed : 23.20 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.03 (0.18), residues: 852 loop : -0.39 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.012 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00310 (15072) covalent geometry : angle 0.56578 (20418) SS BOND : bond 0.00228 ( 30) SS BOND : angle 1.19972 ( 60) hydrogen bonds : bond 0.02583 ( 480) hydrogen bonds : angle 4.84684 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.521 Fit side-chains REVERT: A 64 ASP cc_start: 0.7958 (t0) cc_final: 0.7718 (t0) REVERT: B 64 ASP cc_start: 0.8001 (t0) cc_final: 0.7698 (t0) REVERT: C 64 ASP cc_start: 0.7995 (t0) cc_final: 0.7666 (t0) REVERT: C 152 THR cc_start: 0.8935 (t) cc_final: 0.8097 (p) REVERT: E 64 ASP cc_start: 0.8122 (t0) cc_final: 0.7872 (t0) REVERT: E 98 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7815 (mttm) REVERT: E 152 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8192 (p) REVERT: E 206 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7088 (pp) REVERT: F 64 ASP cc_start: 0.8040 (t0) cc_final: 0.7736 (t0) REVERT: G 81 MET cc_start: 0.7590 (ttm) cc_final: 0.7281 (tmm) REVERT: I 76 MET cc_start: 0.7855 (ttt) cc_final: 0.7393 (ttp) REVERT: J 76 MET cc_start: 0.7668 (ttt) cc_final: 0.7166 (ttp) REVERT: K 76 MET cc_start: 0.7802 (ttp) cc_final: 0.7392 (ttt) REVERT: K 96 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7878 (t) REVERT: L 96 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7548 (t) REVERT: L 120 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7449 (ttpp) outliers start: 59 outliers final: 51 residues processed: 223 average time/residue: 0.1271 time to fit residues: 41.2643 Evaluate side-chains 231 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 68 ASN B 79 ASN C 79 ASN E 79 ASN F 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.179294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131005 restraints weight = 15763.954| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.68 r_work: 0.3104 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15102 Z= 0.159 Angle : 0.573 8.072 20478 Z= 0.294 Chirality : 0.048 0.145 2346 Planarity : 0.003 0.029 2568 Dihedral : 4.132 16.853 2010 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % Rotamer: Outliers : 4.24 % Allowed : 23.03 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 852 loop : -0.39 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 219 TYR 0.013 0.001 TYR G 65 PHE 0.007 0.001 PHE D 198 TRP 0.005 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00376 (15072) covalent geometry : angle 0.56976 (20418) SS BOND : bond 0.00285 ( 30) SS BOND : angle 1.30457 ( 60) hydrogen bonds : bond 0.02671 ( 480) hydrogen bonds : angle 4.79607 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7899 (t0) cc_final: 0.7656 (t0) REVERT: B 64 ASP cc_start: 0.7941 (t0) cc_final: 0.7630 (t0) REVERT: C 64 ASP cc_start: 0.7977 (t0) cc_final: 0.7635 (t0) REVERT: C 152 THR cc_start: 0.8869 (t) cc_final: 0.8038 (p) REVERT: D 64 ASP cc_start: 0.7850 (t0) cc_final: 0.7459 (t0) REVERT: E 64 ASP cc_start: 0.8060 (t0) cc_final: 0.7803 (t0) REVERT: E 98 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7732 (mttm) REVERT: E 152 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 206 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7085 (pp) REVERT: F 64 ASP cc_start: 0.7953 (t0) cc_final: 0.7633 (t0) REVERT: G 81 MET cc_start: 0.7602 (ttm) cc_final: 0.7276 (tmm) REVERT: H 76 MET cc_start: 0.7570 (ttp) cc_final: 0.7142 (ttt) REVERT: H 81 MET cc_start: 0.7610 (ttm) cc_final: 0.7107 (tmm) REVERT: I 76 MET cc_start: 0.7769 (ttt) cc_final: 0.7289 (ttp) REVERT: J 76 MET cc_start: 0.7571 (ttt) cc_final: 0.7060 (ttp) REVERT: K 76 MET cc_start: 0.7690 (ttp) cc_final: 0.7298 (ttt) REVERT: K 96 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7895 (t) REVERT: L 96 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7569 (t) REVERT: L 120 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7295 (ttpp) outliers start: 72 outliers final: 62 residues processed: 235 average time/residue: 0.1337 time to fit residues: 45.6699 Evaluate side-chains 251 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 141 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 79 ASN F 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.179769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131469 restraints weight = 15835.889| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.69 r_work: 0.3110 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15102 Z= 0.130 Angle : 0.567 12.435 20478 Z= 0.289 Chirality : 0.048 0.140 2346 Planarity : 0.003 0.034 2568 Dihedral : 4.096 16.759 2010 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.01 % Favored : 94.66 % Rotamer: Outliers : 3.95 % Allowed : 23.56 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 852 loop : -0.39 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 219 TYR 0.012 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00303 (15072) covalent geometry : angle 0.56432 (20418) SS BOND : bond 0.00223 ( 30) SS BOND : angle 1.19085 ( 60) hydrogen bonds : bond 0.02561 ( 480) hydrogen bonds : angle 4.75061 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.585 Fit side-chains REVERT: A 64 ASP cc_start: 0.7917 (t0) cc_final: 0.7673 (t0) REVERT: B 64 ASP cc_start: 0.7937 (t0) cc_final: 0.7628 (t0) REVERT: B 79 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7965 (t0) REVERT: C 64 ASP cc_start: 0.7972 (t0) cc_final: 0.7626 (t0) REVERT: C 152 THR cc_start: 0.8854 (t) cc_final: 0.8016 (p) REVERT: D 64 ASP cc_start: 0.7810 (t70) cc_final: 0.7440 (t0) REVERT: E 64 ASP cc_start: 0.8077 (t0) cc_final: 0.7818 (t0) REVERT: E 98 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7742 (mttm) REVERT: E 152 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8054 (p) REVERT: E 206 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7099 (pp) REVERT: F 64 ASP cc_start: 0.7938 (t0) cc_final: 0.7622 (t0) REVERT: F 79 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8072 (t0) REVERT: G 81 MET cc_start: 0.7603 (ttm) cc_final: 0.7304 (tmm) REVERT: H 76 MET cc_start: 0.7618 (ttp) cc_final: 0.7166 (ttt) REVERT: H 81 MET cc_start: 0.7618 (ttm) cc_final: 0.7138 (tmm) REVERT: I 76 MET cc_start: 0.7804 (ttt) cc_final: 0.7347 (ttp) REVERT: J 76 MET cc_start: 0.7608 (ttt) cc_final: 0.7109 (ttp) REVERT: K 76 MET cc_start: 0.7752 (ttp) cc_final: 0.7319 (ttt) REVERT: K 96 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7824 (t) REVERT: L 96 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7567 (t) REVERT: L 120 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7328 (ttpp) outliers start: 67 outliers final: 55 residues processed: 240 average time/residue: 0.1346 time to fit residues: 46.7922 Evaluate side-chains 254 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN C 79 ASN H 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.179835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130708 restraints weight = 15794.272| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.42 r_work: 0.3126 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15102 Z= 0.138 Angle : 0.571 12.421 20478 Z= 0.291 Chirality : 0.048 0.139 2346 Planarity : 0.003 0.036 2568 Dihedral : 4.082 16.795 2010 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.84 % Favored : 94.83 % Rotamer: Outliers : 3.83 % Allowed : 23.50 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.02 (0.18), residues: 846 loop : -0.42 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 219 TYR 0.012 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00323 (15072) covalent geometry : angle 0.56763 (20418) SS BOND : bond 0.00238 ( 30) SS BOND : angle 1.21148 ( 60) hydrogen bonds : bond 0.02538 ( 480) hydrogen bonds : angle 4.75374 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.576 Fit side-chains REVERT: A 64 ASP cc_start: 0.7948 (t0) cc_final: 0.7713 (t0) REVERT: B 64 ASP cc_start: 0.7935 (t0) cc_final: 0.7636 (t0) REVERT: C 64 ASP cc_start: 0.7986 (t0) cc_final: 0.7659 (t0) REVERT: C 65 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8365 (mtp-110) REVERT: C 150 ASP cc_start: 0.8615 (t70) cc_final: 0.8379 (t70) REVERT: C 152 THR cc_start: 0.8863 (t) cc_final: 0.8004 (p) REVERT: D 64 ASP cc_start: 0.7863 (t70) cc_final: 0.7494 (t0) REVERT: E 64 ASP cc_start: 0.8103 (t0) cc_final: 0.7847 (t0) REVERT: E 98 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7768 (mttm) REVERT: E 152 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8088 (p) REVERT: E 206 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7108 (pp) REVERT: F 64 ASP cc_start: 0.7962 (t0) cc_final: 0.7654 (t0) REVERT: F 152 THR cc_start: 0.8972 (t) cc_final: 0.8123 (p) REVERT: F 206 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7243 (pp) REVERT: G 81 MET cc_start: 0.7597 (ttm) cc_final: 0.7290 (tmm) REVERT: H 76 MET cc_start: 0.7611 (ttp) cc_final: 0.7159 (ttt) REVERT: H 81 MET cc_start: 0.7589 (ttm) cc_final: 0.7136 (tmm) REVERT: I 76 MET cc_start: 0.7789 (ttt) cc_final: 0.7329 (ttp) REVERT: J 76 MET cc_start: 0.7656 (ttt) cc_final: 0.7152 (ttp) REVERT: K 76 MET cc_start: 0.7754 (ttp) cc_final: 0.7333 (ttt) REVERT: K 96 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7840 (t) REVERT: L 96 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7569 (t) REVERT: L 120 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7381 (ttpp) outliers start: 65 outliers final: 57 residues processed: 239 average time/residue: 0.1362 time to fit residues: 47.2036 Evaluate side-chains 253 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.179365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130392 restraints weight = 15657.594| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.51 r_work: 0.3123 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 15102 Z= 0.163 Angle : 0.797 59.180 20478 Z= 0.448 Chirality : 0.048 0.293 2346 Planarity : 0.003 0.034 2568 Dihedral : 4.114 24.356 2010 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.95 % Favored : 94.72 % Rotamer: Outliers : 3.77 % Allowed : 23.56 % Favored : 72.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.02 (0.18), residues: 846 loop : -0.42 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 219 TYR 0.013 0.001 TYR G 65 PHE 0.006 0.001 PHE D 198 TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00356 (15072) covalent geometry : angle 0.79559 (20418) SS BOND : bond 0.00252 ( 30) SS BOND : angle 1.21233 ( 60) hydrogen bonds : bond 0.02610 ( 480) hydrogen bonds : angle 4.76519 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4767.94 seconds wall clock time: 82 minutes 15.45 seconds (4935.45 seconds total)