Starting phenix.real_space_refine on Fri Jun 13 04:49:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxa_35074/06_2025/8hxa_35074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxa_35074/06_2025/8hxa_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_35074/06_2025/8hxa_35074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxa_35074/06_2025/8hxa_35074.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxa_35074/06_2025/8hxa_35074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxa_35074/06_2025/8hxa_35074.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.88, per 1000 atoms: 0.60 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: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.52 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: 4.99 Time building geometry restraints manager: 3.77 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 2.640 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 35.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (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 TRP 0.019 0.003 TRP H 66 HIS 0.008 0.002 HIS F 117 PHE 0.009 0.002 PHE F 198 TYR 0.020 0.002 TYR B 218 ARG 0.009 0.002 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.20793 ( 480) hydrogen bonds : angle 8.20109 ( 1656) SS BOND : bond 0.02167 ( 30) SS BOND : angle 2.39525 ( 60) covalent geometry : bond 0.00460 (15072) covalent geometry : angle 1.06072 (20418) *********************** 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 : 1.693 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: 0.7710 (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: 0.3214 time to fit residues: 102.4201 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 : 1.637 ------------------------------------------------------------------------------- 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 151 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.185304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133160 restraints weight = 15587.393| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.21 r_work: 0.3187 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15102 Z= 0.155 Angle : 0.682 11.170 20478 Z= 0.339 Chirality : 0.050 0.127 2346 Planarity : 0.003 0.027 2568 Dihedral : 4.522 17.729 2011 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.74 % Favored : 95.93 % Rotamer: Outliers : 3.00 % Allowed : 20.79 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 822 loop : -0.80 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 66 HIS 0.004 0.001 HIS B 117 PHE 0.007 0.001 PHE F 198 TYR 0.014 0.002 TYR D 31 ARG 0.008 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 480) hydrogen bonds : angle 5.76336 ( 1656) SS BOND : bond 0.00286 ( 30) SS BOND : angle 1.80333 ( 60) covalent geometry : bond 0.00354 (15072) covalent geometry : angle 0.67571 (20418) *********************** 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 270 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.579 Fit side-chains REVERT: A 32 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8476 (mtp180) REVERT: A 197 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 32 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8374 (mtp180) REVERT: B 86 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: C 152 THR cc_start: 0.8922 (t) cc_final: 0.8332 (p) REVERT: D 32 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8441 (mtp180) REVERT: D 197 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8406 (p) REVERT: E 152 THR cc_start: 0.8927 (t) cc_final: 0.8367 (p) REVERT: E 206 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6641 (pp) REVERT: F 32 ARG cc_start: 0.8552 (mtm180) cc_final: 0.8287 (mtp180) REVERT: F 152 THR cc_start: 0.8956 (t) cc_final: 0.8381 (p) REVERT: F 197 THR cc_start: 0.8994 (t) cc_final: 0.8608 (p) REVERT: J 81 MET cc_start: 0.7899 (tmm) cc_final: 0.7553 (ttm) REVERT: J 101 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.6110 (pt) REVERT: K 76 MET cc_start: 0.7039 (tpp) cc_final: 0.6803 (ttp) REVERT: K 101 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6216 (pt) REVERT: L 120 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7151 (ttpp) outliers start: 51 outliers final: 30 residues processed: 259 average time/residue: 0.3121 time to fit residues: 113.1917 Evaluate side-chains 251 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 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 121 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 146 SER 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 197 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 146 SER 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 159 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 101 ILE 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 101 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 101 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 0.0060 chunk 161 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.185391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121174 restraints weight = 15646.143| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.07 r_work: 0.3151 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15102 Z= 0.129 Angle : 0.608 11.257 20478 Z= 0.303 Chirality : 0.048 0.134 2346 Planarity : 0.003 0.022 2568 Dihedral : 4.250 15.798 2010 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.02 % Favored : 95.65 % Rotamer: Outliers : 3.65 % Allowed : 20.08 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.14 (0.18), residues: 822 loop : -0.69 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 66 HIS 0.003 0.001 HIS C 117 PHE 0.006 0.001 PHE D 198 TYR 0.014 0.001 TYR A 31 ARG 0.004 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 480) hydrogen bonds : angle 5.32290 ( 1656) SS BOND : bond 0.00205 ( 30) SS BOND : angle 1.17880 ( 60) covalent geometry : bond 0.00298 (15072) covalent geometry : angle 0.60586 (20418) *********************** 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 286 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8703 (mtm180) cc_final: 0.8483 (mtp180) REVERT: B 32 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8430 (mtp180) REVERT: B 64 ASP cc_start: 0.7803 (t0) cc_final: 0.7495 (t0) REVERT: B 86 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: C 64 ASP cc_start: 0.7817 (t0) cc_final: 0.7536 (t0) REVERT: D 32 ARG cc_start: 0.8694 (mtm180) cc_final: 0.8473 (mtp180) REVERT: D 197 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8369 (p) REVERT: E 64 ASP cc_start: 0.7876 (t0) cc_final: 0.7556 (t0) REVERT: E 150 ASP cc_start: 0.8541 (t70) cc_final: 0.8209 (t70) REVERT: E 219 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.8006 (ttp-110) REVERT: F 32 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8334 (mtp180) REVERT: F 206 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7366 (mt) REVERT: J 76 MET cc_start: 0.7454 (ttt) cc_final: 0.7053 (ttp) REVERT: L 120 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7076 (ttpp) outliers start: 62 outliers final: 43 residues processed: 278 average time/residue: 0.3050 time to fit residues: 119.1696 Evaluate side-chains 262 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP 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 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 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 121 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 149 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 124 THR Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 SER 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 130 CYS 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 115 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 149 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 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 59 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.179716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132435 restraints weight = 15623.364| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.82 r_work: 0.3185 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 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 = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15102 Z= 0.191 Angle : 0.635 10.266 20478 Z= 0.319 Chirality : 0.050 0.139 2346 Planarity : 0.003 0.024 2568 Dihedral : 4.255 16.652 2010 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.57 % Favored : 95.10 % Rotamer: Outliers : 5.30 % Allowed : 18.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.02 (0.17), residues: 852 loop : -0.49 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 66 HIS 0.003 0.001 HIS B 176 PHE 0.007 0.001 PHE D 198 TYR 0.015 0.002 TYR A 31 ARG 0.005 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 480) hydrogen bonds : angle 5.18077 ( 1656) SS BOND : bond 0.00335 ( 30) SS BOND : angle 1.47833 ( 60) covalent geometry : bond 0.00461 (15072) covalent geometry : angle 0.63095 (20418) *********************** 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 308 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 218 time to evaluate : 2.236 Fit side-chains REVERT: A 32 ARG cc_start: 0.8872 (mtm180) cc_final: 0.8663 (mtp180) REVERT: A 64 ASP cc_start: 0.7952 (t0) cc_final: 0.7698 (t0) REVERT: B 32 ARG cc_start: 0.8832 (mtm180) cc_final: 0.8601 (mtp180) REVERT: B 64 ASP cc_start: 0.7974 (t0) cc_final: 0.7722 (t0) REVERT: C 64 ASP cc_start: 0.8043 (t0) cc_final: 0.7748 (t0) REVERT: D 32 ARG cc_start: 0.8848 (mtm180) cc_final: 0.8644 (mtp180) REVERT: E 64 ASP cc_start: 0.8057 (t0) cc_final: 0.7794 (t0) REVERT: E 98 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7916 (mttm) REVERT: E 152 THR cc_start: 0.8981 (t) cc_final: 0.8324 (p) REVERT: E 206 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.6972 (pp) REVERT: F 32 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8554 (mtp180) REVERT: F 64 ASP cc_start: 0.8004 (t0) cc_final: 0.7757 (t0) REVERT: I 76 MET cc_start: 0.7949 (ttt) cc_final: 0.7492 (ttp) REVERT: J 68 LYS cc_start: 0.7772 (pttp) cc_final: 0.7532 (ptmm) REVERT: J 76 MET cc_start: 0.7777 (ttt) cc_final: 0.7245 (ttp) REVERT: J 96 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7654 (t) REVERT: K 76 MET cc_start: 0.7858 (ttp) cc_final: 0.7519 (ttt) REVERT: K 96 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7847 (t) REVERT: L 120 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7495 (ttpp) outliers start: 90 outliers final: 70 residues processed: 292 average time/residue: 0.3303 time to fit residues: 141.7260 Evaluate side-chains 275 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 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 146 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 ILE 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 146 SER Chi-restraints excluded: chain C residue 149 CYS 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 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 124 THR 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 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 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 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 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 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 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 35 optimal weight: 0.0770 chunk 132 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 79 ASN C 68 ASN C 79 ASN C 110 GLN E 68 ASN E 79 ASN F 68 ASN F 79 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131917 restraints weight = 15825.517| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.72 r_work: 0.3098 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 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 = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15102 Z= 0.168 Angle : 0.595 8.023 20478 Z= 0.304 Chirality : 0.049 0.140 2346 Planarity : 0.003 0.022 2568 Dihedral : 4.229 16.663 2010 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.35 % Favored : 95.32 % Rotamer: Outliers : 5.30 % Allowed : 20.67 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.02 (0.17), residues: 852 loop : -0.43 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 66 HIS 0.003 0.001 HIS C 173 PHE 0.007 0.001 PHE D 198 TYR 0.013 0.001 TYR G 65 ARG 0.006 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 480) hydrogen bonds : angle 4.99239 ( 1656) SS BOND : bond 0.00320 ( 30) SS BOND : angle 1.35803 ( 60) covalent geometry : bond 0.00400 (15072) covalent geometry : angle 0.59110 (20418) *********************** 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 286 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 1.777 Fit side-chains REVERT: A 64 ASP cc_start: 0.7909 (t0) cc_final: 0.7648 (t0) REVERT: B 64 ASP cc_start: 0.7926 (t0) cc_final: 0.7652 (t0) REVERT: C 64 ASP cc_start: 0.7958 (t0) cc_final: 0.7668 (t0) REVERT: C 65 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8327 (mtp-110) REVERT: E 64 ASP cc_start: 0.8010 (t0) cc_final: 0.7710 (t0) REVERT: E 98 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7750 (mttm) REVERT: E 152 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8199 (p) REVERT: E 206 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.6939 (pp) REVERT: F 32 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8418 (mtp180) REVERT: F 64 ASP cc_start: 0.7968 (t0) cc_final: 0.7667 (t0) REVERT: I 76 MET cc_start: 0.7824 (ttt) cc_final: 0.7299 (ttp) REVERT: J 76 MET cc_start: 0.7643 (ttt) cc_final: 0.7089 (ttp) REVERT: K 76 MET cc_start: 0.7783 (ttp) cc_final: 0.7420 (ttt) REVERT: L 120 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7259 (ttpp) outliers start: 90 outliers final: 66 residues processed: 272 average time/residue: 0.3313 time to fit residues: 130.0649 Evaluate side-chains 253 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 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 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 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 146 SER 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 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 130 CYS 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 79 ASN 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 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 VAL 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 F residue 206 LEU 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 H residue 137 SER 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 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 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 B 79 ASN C 79 ASN C 110 GLN E 79 ASN F 79 ASN K 37 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.183565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135025 restraints weight = 15681.640| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.44 r_work: 0.3128 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2491 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= 0.124 Angle : 0.569 8.585 20478 Z= 0.290 Chirality : 0.048 0.140 2346 Planarity : 0.003 0.028 2568 Dihedral : 4.149 16.755 2010 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.94 % Rotamer: Outliers : 4.65 % Allowed : 21.85 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.03 (0.17), residues: 852 loop : -0.42 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 PHE 0.006 0.001 PHE D 198 TYR 0.012 0.001 TYR G 65 ARG 0.007 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 480) hydrogen bonds : angle 4.90896 ( 1656) SS BOND : bond 0.00209 ( 30) SS BOND : angle 1.16464 ( 60) covalent geometry : bond 0.00285 (15072) covalent geometry : angle 0.56659 (20418) *********************** 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 264 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 185 time to evaluate : 1.628 Fit side-chains REVERT: A 64 ASP cc_start: 0.7859 (t0) cc_final: 0.7611 (t0) REVERT: B 64 ASP cc_start: 0.7934 (t0) cc_final: 0.7661 (t0) REVERT: B 189 SER cc_start: 0.9072 (m) cc_final: 0.8845 (t) REVERT: C 64 ASP cc_start: 0.7928 (t0) cc_final: 0.7634 (t0) REVERT: C 65 ARG cc_start: 0.8534 (mtm180) cc_final: 0.8315 (mtp-110) REVERT: E 64 ASP cc_start: 0.8013 (t0) cc_final: 0.7761 (t0) REVERT: E 98 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7726 (mttm) REVERT: E 152 THR cc_start: 0.8871 (t) cc_final: 0.8208 (p) REVERT: E 206 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.6934 (pp) REVERT: F 32 ARG cc_start: 0.8655 (mtm180) cc_final: 0.8406 (mtp180) REVERT: F 64 ASP cc_start: 0.7955 (t0) cc_final: 0.7669 (t0) REVERT: I 76 MET cc_start: 0.7758 (ttt) cc_final: 0.7240 (ttp) REVERT: J 76 MET cc_start: 0.7596 (ttt) cc_final: 0.7048 (ttp) REVERT: K 76 MET cc_start: 0.7731 (ttp) cc_final: 0.7357 (ttt) REVERT: L 120 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7716 (ttmm) outliers start: 79 outliers final: 64 residues processed: 249 average time/residue: 0.2651 time to fit residues: 96.5297 Evaluate side-chains 248 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 169 LYS 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 130 CYS Chi-restraints excluded: chain B residue 149 CYS 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 146 SER 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 59 SER 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 124 THR Chi-restraints excluded: chain D residue 130 CYS 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 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 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 146 SER Chi-restraints excluded: chain F residue 159 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 79 ASN C 110 GLN E 79 ASN F 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.180998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131887 restraints weight = 15723.666| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.43 r_work: 0.3179 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15102 Z= 0.122 Angle : 0.556 8.825 20478 Z= 0.284 Chirality : 0.047 0.139 2346 Planarity : 0.003 0.030 2568 Dihedral : 4.098 16.615 2010 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Rotamer: Outliers : 4.36 % Allowed : 22.38 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.01 (0.18), residues: 852 loop : -0.41 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 66 HIS 0.003 0.001 HIS I 130 PHE 0.006 0.001 PHE D 198 TYR 0.012 0.001 TYR G 65 ARG 0.008 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 480) hydrogen bonds : angle 4.83564 ( 1656) SS BOND : bond 0.00200 ( 30) SS BOND : angle 1.13563 ( 60) covalent geometry : bond 0.00281 (15072) covalent geometry : angle 0.55338 (20418) *********************** 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 258 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 184 time to evaluate : 1.555 Fit side-chains REVERT: A 64 ASP cc_start: 0.7954 (t0) cc_final: 0.7743 (t0) REVERT: B 64 ASP cc_start: 0.8037 (t0) cc_final: 0.7832 (t0) REVERT: C 64 ASP cc_start: 0.8049 (t0) cc_final: 0.7780 (t0) REVERT: C 65 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8409 (mtp-110) REVERT: E 64 ASP cc_start: 0.8129 (t0) cc_final: 0.7896 (t0) REVERT: E 80 MET cc_start: 0.8564 (ttt) cc_final: 0.8337 (ttt) REVERT: E 98 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7880 (mttm) REVERT: E 152 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8273 (p) REVERT: E 206 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7110 (pp) REVERT: F 32 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8520 (mtp180) REVERT: F 64 ASP cc_start: 0.8040 (t0) cc_final: 0.7784 (t0) REVERT: G 81 MET cc_start: 0.7600 (ttm) cc_final: 0.7333 (tmm) REVERT: I 76 MET cc_start: 0.7891 (ttt) cc_final: 0.7426 (ttp) REVERT: J 76 MET cc_start: 0.7750 (ttt) cc_final: 0.7236 (ttp) REVERT: K 76 MET cc_start: 0.7887 (ttp) cc_final: 0.7463 (ttt) REVERT: L 120 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7579 (ttpp) outliers start: 74 outliers final: 65 residues processed: 243 average time/residue: 0.2717 time to fit residues: 96.1230 Evaluate side-chains 243 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 124 THR 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 169 LYS 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 B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 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 159 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 59 SER 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 124 THR Chi-restraints excluded: chain D residue 130 CYS 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 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 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 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 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 L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 79 ASN C 110 GLN E 79 ASN F 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130203 restraints weight = 15714.695| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.39 r_work: 0.3116 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15102 Z= 0.195 Angle : 0.591 8.021 20478 Z= 0.303 Chirality : 0.049 0.137 2346 Planarity : 0.003 0.029 2568 Dihedral : 4.170 16.925 2010 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 4.77 % Allowed : 22.32 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.06 (0.18), residues: 852 loop : -0.43 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 PHE 0.007 0.001 PHE A 198 TYR 0.015 0.002 TYR G 65 ARG 0.009 0.001 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.02817 ( 480) hydrogen bonds : angle 4.86780 ( 1656) SS BOND : bond 0.00332 ( 30) SS BOND : angle 1.37878 ( 60) covalent geometry : bond 0.00469 (15072) covalent geometry : angle 0.58681 (20418) *********************** 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 258 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 177 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7927 (t0) cc_final: 0.7720 (t0) REVERT: B 64 ASP cc_start: 0.8003 (t0) cc_final: 0.7800 (t0) REVERT: C 64 ASP cc_start: 0.8049 (t0) cc_final: 0.7772 (t0) REVERT: C 65 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8447 (mtp-110) REVERT: D 64 ASP cc_start: 0.7902 (t70) cc_final: 0.7536 (t0) REVERT: E 64 ASP cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: E 98 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7839 (mttm) REVERT: E 150 ASP cc_start: 0.8733 (t70) cc_final: 0.8444 (t70) REVERT: E 152 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8192 (p) REVERT: E 206 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7143 (pp) REVERT: F 32 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8517 (mtp180) REVERT: F 64 ASP cc_start: 0.8008 (t0) cc_final: 0.7772 (t0) REVERT: G 81 MET cc_start: 0.7629 (ttm) cc_final: 0.7334 (tmm) REVERT: I 76 MET cc_start: 0.7906 (ttt) cc_final: 0.7423 (ttp) REVERT: J 76 MET cc_start: 0.7790 (ttt) cc_final: 0.7247 (ttp) REVERT: K 76 MET cc_start: 0.7888 (ttp) cc_final: 0.7453 (ttt) REVERT: L 96 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7521 (t) REVERT: L 120 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7541 (ttpp) outliers start: 81 outliers final: 69 residues processed: 246 average time/residue: 0.2692 time to fit residues: 96.8900 Evaluate side-chains 250 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 48 ILE 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 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 60 GLU 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 B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 48 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 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 D residue 197 THR Chi-restraints excluded: chain E residue 48 ILE 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 121 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 149 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 48 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 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 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 130 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.178982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129866 restraints weight = 15652.011| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.49 r_work: 0.3112 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 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 = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2729 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= 0.145 Angle : 0.571 9.098 20478 Z= 0.293 Chirality : 0.048 0.139 2346 Planarity : 0.003 0.036 2568 Dihedral : 4.154 16.825 2010 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % Rotamer: Outliers : 4.18 % Allowed : 22.85 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.12 (0.18), residues: 846 loop : -0.45 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 66 HIS 0.003 0.001 HIS I 130 PHE 0.006 0.001 PHE D 198 TYR 0.013 0.001 TYR G 65 ARG 0.009 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 480) hydrogen bonds : angle 4.81770 ( 1656) SS BOND : bond 0.00242 ( 30) SS BOND : angle 1.23144 ( 60) covalent geometry : bond 0.00342 (15072) covalent geometry : angle 0.56827 (20418) *********************** 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 256 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 185 time to evaluate : 1.727 Fit side-chains REVERT: A 64 ASP cc_start: 0.7860 (t0) cc_final: 0.7642 (t0) REVERT: B 64 ASP cc_start: 0.7949 (t0) cc_final: 0.7714 (t0) REVERT: B 98 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7693 (mttm) REVERT: C 64 ASP cc_start: 0.8014 (t0) cc_final: 0.7721 (t0) REVERT: C 65 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8352 (mtp-110) REVERT: D 64 ASP cc_start: 0.7805 (t70) cc_final: 0.7441 (t0) REVERT: E 64 ASP cc_start: 0.8021 (t0) cc_final: 0.7767 (t0) REVERT: E 98 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7730 (mttm) REVERT: E 150 ASP cc_start: 0.8693 (t70) cc_final: 0.8383 (t70) REVERT: E 152 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8106 (p) REVERT: E 206 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7113 (pp) REVERT: F 32 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8467 (mtp180) REVERT: F 64 ASP cc_start: 0.7939 (t0) cc_final: 0.7670 (t0) REVERT: F 206 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7310 (pp) REVERT: G 81 MET cc_start: 0.7613 (ttm) cc_final: 0.7301 (tmm) REVERT: H 81 MET cc_start: 0.7631 (ttm) cc_final: 0.7129 (tmm) REVERT: I 76 MET cc_start: 0.7762 (ttt) cc_final: 0.7258 (ttp) REVERT: J 76 MET cc_start: 0.7631 (ttt) cc_final: 0.7068 (ttp) REVERT: J 96 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7672 (t) REVERT: K 76 MET cc_start: 0.7687 (ttp) cc_final: 0.7288 (ttt) REVERT: L 120 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7320 (ttpp) outliers start: 71 outliers final: 62 residues processed: 244 average time/residue: 0.2763 time to fit residues: 97.9658 Evaluate side-chains 253 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 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 B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 48 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 23 THR Chi-restraints excluded: chain D residue 48 ILE 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 130 CYS 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 121 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 149 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 48 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 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 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 Chi-restraints excluded: chain L residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 110 GLN E 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.181015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132022 restraints weight = 15721.593| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.42 r_work: 0.3102 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: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2844 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 : 0.575 8.943 20478 Z= 0.296 Chirality : 0.048 0.139 2346 Planarity : 0.003 0.034 2568 Dihedral : 4.179 17.105 2010 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.95 % Favored : 94.72 % Rotamer: Outliers : 4.18 % Allowed : 22.91 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.15 (0.18), residues: 846 loop : -0.48 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.003 0.001 HIS I 130 PHE 0.006 0.001 PHE D 198 TYR 0.013 0.001 TYR G 65 ARG 0.010 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.02674 ( 480) hydrogen bonds : angle 4.80928 ( 1656) SS BOND : bond 0.00270 ( 30) SS BOND : angle 1.26600 ( 60) covalent geometry : bond 0.00377 (15072) covalent geometry : angle 0.57210 (20418) ********************** 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 266 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 195 time to evaluate : 2.440 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7919 (t0) cc_final: 0.7701 (t0) REVERT: B 64 ASP cc_start: 0.8016 (t0) cc_final: 0.7792 (t0) REVERT: B 98 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7677 (mttm) REVERT: C 64 ASP cc_start: 0.8031 (t0) cc_final: 0.7744 (t0) REVERT: C 65 ARG cc_start: 0.8637 (mtm180) cc_final: 0.8385 (mtp-110) REVERT: C 152 THR cc_start: 0.8873 (t) cc_final: 0.8044 (p) REVERT: D 64 ASP cc_start: 0.7923 (t70) cc_final: 0.7562 (t0) REVERT: E 64 ASP cc_start: 0.8053 (t0) cc_final: 0.7798 (t0) REVERT: E 98 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7726 (mttm) REVERT: E 150 ASP cc_start: 0.8687 (t70) cc_final: 0.8410 (t70) REVERT: E 152 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8088 (p) REVERT: E 206 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7092 (pp) REVERT: F 32 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8471 (mtp180) REVERT: F 64 ASP cc_start: 0.7991 (t0) cc_final: 0.7712 (t0) REVERT: F 152 THR cc_start: 0.8898 (t) cc_final: 0.8066 (p) REVERT: F 206 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7336 (pp) REVERT: G 81 MET cc_start: 0.7440 (ttm) cc_final: 0.7157 (tmm) REVERT: H 81 MET cc_start: 0.7357 (ttm) cc_final: 0.6981 (tmm) REVERT: I 76 MET cc_start: 0.7669 (ttt) cc_final: 0.7166 (ttp) REVERT: J 76 MET cc_start: 0.7598 (ttt) cc_final: 0.7035 (ttp) REVERT: J 96 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7689 (t) REVERT: K 76 MET cc_start: 0.7680 (ttp) cc_final: 0.7305 (ttt) REVERT: L 120 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7737 (ttmm) outliers start: 71 outliers final: 61 residues processed: 256 average time/residue: 0.2724 time to fit residues: 102.0087 Evaluate side-chains 255 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 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 B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 48 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 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 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 121 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 149 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 48 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 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 96 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.181604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133394 restraints weight = 15706.753| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.59 r_work: 0.3136 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 15102 Z= 0.232 Angle : 0.830 59.200 20478 Z= 0.468 Chirality : 0.062 1.826 2346 Planarity : 0.004 0.160 2568 Dihedral : 4.223 26.826 2010 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 4.00 % Allowed : 23.14 % Favored : 72.85 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.16 (0.18), residues: 846 loop : -0.48 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.003 0.001 HIS I 130 PHE 0.006 0.001 PHE A 198 TYR 0.014 0.001 TYR G 65 ARG 0.008 0.001 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 480) hydrogen bonds : angle 4.85365 ( 1656) SS BOND : bond 0.00307 ( 30) SS BOND : angle 1.25367 ( 60) covalent geometry : bond 0.00507 (15072) covalent geometry : angle 0.82795 (20418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9999.78 seconds wall clock time: 173 minutes 31.08 seconds (10411.08 seconds total)