Starting phenix.real_space_refine on Fri Feb 16 08:28:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_35074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_35074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_35074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_35074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxa_35074/02_2024/8hxa_35074.pdb" } 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 Residue "B ARG 219": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.09, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.40 Conformation dependent library (CDL) restraints added in 2.6 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: 2.00 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: 5.23 Time building geometry restraints manager: 5.92 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: 98.76 - 105.85: 256 105.85 - 112.94: 8116 112.94 - 120.03: 5126 120.03 - 127.12: 6754 127.12 - 134.21: 166 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 2.520 nonbonded pdb=" NH2 ARG D 32 " pdb=" OE2 GLU E 127 " model vdw 2.309 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 7.630 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 41.090 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- 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 0.057 15072 Z= 0.293 Angle : 1.061 15.052 20418 Z= 0.527 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.701 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: 0.3265 time to fit residues: 104.5062 Evaluate side-chains 222 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 129 ASN E 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15072 Z= 0.189 Angle : 0.637 10.908 20418 Z= 0.316 Chirality : 0.049 0.133 2346 Planarity : 0.003 0.026 2568 Dihedral : 4.474 18.138 2011 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.80 % Favored : 95.87 % Rotamer: Outliers : 2.83 % Allowed : 21.32 % 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: -0.47 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: 0.18 (0.18), residues: 810 loop : -0.69 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.003 0.001 HIS A 57 PHE 0.006 0.001 PHE F 198 TYR 0.012 0.001 TYR D 31 ARG 0.006 0.001 ARG E 219 *********************** 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 273 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 225 time to evaluate : 1.702 Fit side-chains REVERT: A 197 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8682 (p) REVERT: B 169 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7985 (ptpp) REVERT: C 152 THR cc_start: 0.8995 (t) cc_final: 0.8467 (p) REVERT: D 197 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8520 (p) REVERT: E 152 THR cc_start: 0.9033 (t) cc_final: 0.8526 (p) REVERT: F 152 THR cc_start: 0.8999 (t) cc_final: 0.8496 (p) REVERT: F 169 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7879 (ptpp) REVERT: F 197 THR cc_start: 0.9148 (t) cc_final: 0.8741 (p) REVERT: J 81 MET cc_start: 0.7473 (tmm) cc_final: 0.7193 (ttm) REVERT: J 101 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7319 (pt) REVERT: K 101 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7337 (pt) REVERT: L 101 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7385 (pt) REVERT: L 120 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7985 (ttpp) outliers start: 48 outliers final: 26 residues processed: 265 average time/residue: 0.3203 time to fit residues: 118.8982 Evaluate side-chains 245 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 23 THR 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 120 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER 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 J residue 137 SER 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 101 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 55 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 129 ASN E 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15072 Z= 0.331 Angle : 0.662 11.128 20418 Z= 0.331 Chirality : 0.050 0.138 2346 Planarity : 0.003 0.027 2568 Dihedral : 4.403 16.114 2010 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.18 % Favored : 95.49 % Rotamer: Outliers : 5.36 % Allowed : 20.32 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.17), residues: 834 loop : -0.67 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 66 HIS 0.003 0.001 HIS C 176 PHE 0.006 0.001 PHE C 198 TYR 0.018 0.002 TYR D 31 ARG 0.005 0.001 ARG A 219 *********************** 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 305 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 214 time to evaluate : 1.597 Fit side-chains REVERT: B 178 LYS cc_start: 0.7201 (mmtm) cc_final: 0.7000 (mmtt) REVERT: C 64 ASP cc_start: 0.7852 (t0) cc_final: 0.7631 (t0) REVERT: C 152 THR cc_start: 0.9063 (t) cc_final: 0.8440 (p) REVERT: E 64 ASP cc_start: 0.7923 (t0) cc_final: 0.7647 (t0) REVERT: E 150 ASP cc_start: 0.8690 (t70) cc_final: 0.8363 (t70) REVERT: E 152 THR cc_start: 0.9074 (t) cc_final: 0.8464 (p) REVERT: F 152 THR cc_start: 0.9057 (t) cc_final: 0.8451 (p) REVERT: F 197 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8696 (p) REVERT: F 206 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7466 (mt) REVERT: J 101 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7388 (pt) REVERT: K 76 MET cc_start: 0.8300 (ttp) cc_final: 0.8013 (ttm) REVERT: L 120 LYS cc_start: 0.8521 (ttmt) cc_final: 0.7991 (ttpp) outliers start: 91 outliers final: 60 residues processed: 294 average time/residue: 0.2946 time to fit residues: 124.0613 Evaluate side-chains 261 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 198 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 175 LEU 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 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 ILE 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 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 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 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 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 62 THR Chi-restraints excluded: chain J residue 101 ILE 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 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15072 Z= 0.328 Angle : 0.626 10.021 20418 Z= 0.317 Chirality : 0.050 0.141 2346 Planarity : 0.003 0.027 2568 Dihedral : 4.371 16.754 2010 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.40 % Favored : 95.27 % Rotamer: Outliers : 4.59 % Allowed : 22.56 % Favored : 72.85 % 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: -0.52 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.10 (0.17), residues: 864 loop : -0.48 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 66 HIS 0.004 0.001 HIS F 173 PHE 0.008 0.001 PHE C 89 TYR 0.016 0.002 TYR J 121 ARG 0.009 0.001 ARG F 219 *********************** 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 271 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 193 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 175 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7736 (mm) REVERT: B 64 ASP cc_start: 0.7908 (t0) cc_final: 0.7681 (t0) REVERT: C 64 ASP cc_start: 0.7988 (t0) cc_final: 0.7731 (t0) REVERT: C 152 THR cc_start: 0.9051 (t) cc_final: 0.8382 (p) REVERT: E 64 ASP cc_start: 0.7947 (t0) cc_final: 0.7698 (t0) REVERT: E 152 THR cc_start: 0.9061 (t) cc_final: 0.8454 (p) REVERT: F 64 ASP cc_start: 0.7950 (t0) cc_final: 0.7695 (t0) REVERT: F 152 THR cc_start: 0.9053 (t) cc_final: 0.8397 (p) REVERT: J 77 MET cc_start: 0.7922 (mtt) cc_final: 0.7689 (mtp) REVERT: K 76 MET cc_start: 0.8338 (ttp) cc_final: 0.7720 (ttt) REVERT: L 120 LYS cc_start: 0.8537 (ttmt) cc_final: 0.7987 (ttpp) outliers start: 78 outliers final: 64 residues processed: 262 average time/residue: 0.2891 time to fit residues: 109.6100 Evaluate side-chains 250 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 120 SER 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 175 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 23 THR 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 159 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 120 SER 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 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 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 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 96 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 101 ILE 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 96 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 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 68 ASN C 79 ASN D 68 ASN D 79 ASN E 68 ASN E 79 ASN F 68 ASN F 79 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15072 Z= 0.284 Angle : 0.593 12.297 20418 Z= 0.301 Chirality : 0.049 0.141 2346 Planarity : 0.003 0.026 2568 Dihedral : 4.276 16.801 2010 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.94 % Rotamer: Outliers : 5.30 % Allowed : 22.79 % Favored : 71.91 % 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: -0.53 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.12 (0.17), residues: 864 loop : -0.47 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 66 HIS 0.004 0.001 HIS I 130 PHE 0.006 0.001 PHE A 198 TYR 0.014 0.001 TYR G 65 ARG 0.006 0.001 ARG C 219 *********************** 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 282 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 192 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: B 64 ASP cc_start: 0.7932 (t0) cc_final: 0.7688 (t0) REVERT: C 64 ASP cc_start: 0.8008 (t0) cc_final: 0.7779 (t0) REVERT: C 152 THR cc_start: 0.9033 (t) cc_final: 0.8321 (p) REVERT: D 64 ASP cc_start: 0.7851 (t0) cc_final: 0.7547 (t0) REVERT: D 175 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7837 (mm) REVERT: E 64 ASP cc_start: 0.7986 (t0) cc_final: 0.7738 (t0) REVERT: E 152 THR cc_start: 0.9041 (t) cc_final: 0.8371 (p) REVERT: F 64 ASP cc_start: 0.8003 (t0) cc_final: 0.7756 (t0) REVERT: F 152 THR cc_start: 0.9043 (t) cc_final: 0.8325 (p) REVERT: K 76 MET cc_start: 0.8336 (ttp) cc_final: 0.7725 (ttt) outliers start: 90 outliers final: 69 residues processed: 270 average time/residue: 0.2940 time to fit residues: 114.4334 Evaluate side-chains 251 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 181 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 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 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 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 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 175 LEU 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 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 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL 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 I residue 59 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 68 ASN B 79 ASN C 79 ASN D 79 ASN E 79 ASN F 79 ASN H 37 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15072 Z= 0.177 Angle : 0.560 12.174 20418 Z= 0.283 Chirality : 0.047 0.141 2346 Planarity : 0.003 0.028 2568 Dihedral : 4.153 16.533 2010 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.46 % Favored : 95.21 % Rotamer: Outliers : 3.95 % Allowed : 24.20 % Favored : 71.85 % 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: -0.49 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.10 (0.17), residues: 864 loop : -0.44 (0.21), residues: 954 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 0.005 0.001 PHE D 198 TYR 0.012 0.001 TYR G 65 ARG 0.007 0.000 ARG F 219 *********************** 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 249 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 182 time to evaluate : 1.784 Fit side-chains REVERT: B 64 ASP cc_start: 0.7922 (t0) cc_final: 0.7679 (t0) REVERT: C 64 ASP cc_start: 0.7984 (t0) cc_final: 0.7740 (t0) REVERT: C 152 THR cc_start: 0.9023 (t) cc_final: 0.8294 (p) REVERT: D 64 ASP cc_start: 0.7902 (t0) cc_final: 0.7566 (t0) REVERT: D 175 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7818 (mm) REVERT: E 64 ASP cc_start: 0.7940 (t0) cc_final: 0.7690 (t0) REVERT: E 152 THR cc_start: 0.9027 (t) cc_final: 0.8336 (p) REVERT: F 64 ASP cc_start: 0.7962 (t0) cc_final: 0.7722 (t0) REVERT: F 152 THR cc_start: 0.9025 (t) cc_final: 0.8306 (p) REVERT: G 77 MET cc_start: 0.6888 (mmm) cc_final: 0.6438 (mmm) REVERT: K 76 MET cc_start: 0.8265 (ttp) cc_final: 0.7647 (ttt) REVERT: L 120 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8031 (ttpp) outliers start: 67 outliers final: 60 residues processed: 236 average time/residue: 0.3242 time to fit residues: 109.9717 Evaluate side-chains 240 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 179 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 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 147 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 79 ASN 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 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 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 175 LEU 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 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 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 110 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS C 79 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS D 79 ASN D 184 HIS E 79 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS F 79 ASN ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 15072 Z= 0.590 Angle : 0.709 12.107 20418 Z= 0.362 Chirality : 0.054 0.149 2346 Planarity : 0.004 0.032 2568 Dihedral : 4.556 17.581 2010 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.94 % Rotamer: Outliers : 5.65 % Allowed : 24.09 % Favored : 70.26 % 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: -0.77 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.33 (0.17), residues: 858 loop : -0.59 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 34 HIS 0.006 0.001 HIS B 173 PHE 0.011 0.002 PHE C 89 TYR 0.020 0.002 TYR G 65 ARG 0.010 0.001 ARG C 219 *********************** 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 277 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 181 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8014 (t0) cc_final: 0.7687 (t0) REVERT: B 64 ASP cc_start: 0.8000 (t0) cc_final: 0.7768 (t0) REVERT: C 152 THR cc_start: 0.8962 (t) cc_final: 0.8221 (p) REVERT: D 64 ASP cc_start: 0.8019 (t0) cc_final: 0.7716 (t0) REVERT: E 64 ASP cc_start: 0.7998 (t0) cc_final: 0.7755 (t0) REVERT: E 152 THR cc_start: 0.8984 (t) cc_final: 0.8278 (p) REVERT: F 64 ASP cc_start: 0.7997 (t0) cc_final: 0.7785 (t0) REVERT: F 152 THR cc_start: 0.8948 (t) cc_final: 0.8203 (p) REVERT: F 206 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7464 (pp) REVERT: K 76 MET cc_start: 0.8316 (ttp) cc_final: 0.7703 (ttt) outliers start: 96 outliers final: 77 residues processed: 267 average time/residue: 0.3024 time to fit residues: 121.0450 Evaluate side-chains 256 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 178 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 147 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 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 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 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 159 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 96 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 62 THR Chi-restraints excluded: chain H residue 96 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 I residue 59 LEU Chi-restraints excluded: chain I residue 96 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 35 VAL Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 79 ASN E 79 ASN F 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15072 Z= 0.226 Angle : 0.585 11.697 20418 Z= 0.297 Chirality : 0.048 0.142 2346 Planarity : 0.003 0.031 2568 Dihedral : 4.299 17.147 2010 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.40 % Favored : 95.27 % Rotamer: Outliers : 4.06 % Allowed : 25.80 % Favored : 70.14 % 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: -0.73 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.18 (0.18), residues: 828 loop : -0.69 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 66 HIS 0.004 0.001 HIS I 130 PHE 0.005 0.001 PHE G 93 TYR 0.012 0.001 TYR G 65 ARG 0.009 0.001 ARG C 219 *********************** 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 253 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 184 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7978 (t0) cc_final: 0.7669 (t0) REVERT: B 64 ASP cc_start: 0.7951 (t0) cc_final: 0.7718 (t0) REVERT: C 152 THR cc_start: 0.8965 (t) cc_final: 0.8186 (p) REVERT: D 64 ASP cc_start: 0.7991 (t0) cc_final: 0.7692 (t0) REVERT: E 64 ASP cc_start: 0.7930 (t0) cc_final: 0.7690 (t0) REVERT: E 150 ASP cc_start: 0.8646 (t70) cc_final: 0.8337 (t70) REVERT: E 152 THR cc_start: 0.8972 (t) cc_final: 0.8232 (p) REVERT: F 64 ASP cc_start: 0.7933 (t0) cc_final: 0.7724 (t0) REVERT: F 152 THR cc_start: 0.8933 (t) cc_final: 0.8164 (p) REVERT: F 206 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7430 (pp) REVERT: H 76 MET cc_start: 0.8143 (ttp) cc_final: 0.7684 (ttt) REVERT: K 76 MET cc_start: 0.8290 (ttp) cc_final: 0.7661 (ttt) REVERT: L 120 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8056 (ttpp) outliers start: 69 outliers final: 61 residues processed: 244 average time/residue: 0.2941 time to fit residues: 104.0820 Evaluate side-chains 241 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 179 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 SER 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 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 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 F residue 24 ILE Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain 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 35 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.4980 chunk 166 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15072 Z= 0.199 Angle : 0.567 12.275 20418 Z= 0.288 Chirality : 0.047 0.142 2346 Planarity : 0.003 0.031 2568 Dihedral : 4.197 17.017 2010 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Rotamer: Outliers : 3.59 % Allowed : 26.33 % Favored : 70.08 % 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: -0.70 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.15 (0.18), residues: 828 loop : -0.68 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 66 HIS 0.004 0.001 HIS I 130 PHE 0.005 0.001 PHE D 198 TYR 0.011 0.001 TYR G 65 ARG 0.008 0.000 ARG C 219 *********************** 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 242 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 181 time to evaluate : 1.721 Fit side-chains REVERT: A 64 ASP cc_start: 0.7959 (t0) cc_final: 0.7666 (t0) REVERT: B 64 ASP cc_start: 0.7932 (t0) cc_final: 0.7702 (t0) REVERT: B 126 MET cc_start: 0.8615 (mmm) cc_final: 0.8395 (mmm) REVERT: C 152 THR cc_start: 0.8945 (t) cc_final: 0.8172 (p) REVERT: D 64 ASP cc_start: 0.7976 (t0) cc_final: 0.7682 (t0) REVERT: E 64 ASP cc_start: 0.7916 (t0) cc_final: 0.7683 (t0) REVERT: E 150 ASP cc_start: 0.8651 (t70) cc_final: 0.8344 (t70) REVERT: E 152 THR cc_start: 0.8951 (t) cc_final: 0.8223 (p) REVERT: F 64 ASP cc_start: 0.7935 (t0) cc_final: 0.7721 (t0) REVERT: F 152 THR cc_start: 0.8917 (t) cc_final: 0.8144 (p) REVERT: F 206 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7438 (pp) REVERT: H 76 MET cc_start: 0.8163 (ttp) cc_final: 0.7678 (ttt) REVERT: K 76 MET cc_start: 0.8318 (ttp) cc_final: 0.7686 (ttt) REVERT: L 120 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8049 (ttpp) outliers start: 61 outliers final: 58 residues processed: 234 average time/residue: 0.3084 time to fit residues: 103.6416 Evaluate side-chains 240 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 SER 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 149 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 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 F residue 24 ILE Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain 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 35 VAL 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 170 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 79 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15072 Z= 0.182 Angle : 0.562 13.389 20418 Z= 0.282 Chirality : 0.047 0.142 2346 Planarity : 0.003 0.036 2568 Dihedral : 4.125 16.781 2010 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.95 % Favored : 94.72 % Rotamer: Outliers : 3.59 % Allowed : 26.21 % Favored : 70.20 % 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: -0.67 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.11 (0.18), residues: 816 loop : -0.67 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 66 HIS 0.004 0.001 HIS I 130 PHE 0.006 0.001 PHE G 93 TYR 0.011 0.001 TYR L 65 ARG 0.009 0.000 ARG F 219 ********************** 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 246 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 185 time to evaluate : 1.753 Fit side-chains REVERT: A 64 ASP cc_start: 0.7937 (t0) cc_final: 0.7663 (t0) REVERT: B 64 ASP cc_start: 0.7908 (t0) cc_final: 0.7682 (t0) REVERT: B 126 MET cc_start: 0.8619 (mmm) cc_final: 0.8389 (mmm) REVERT: C 152 THR cc_start: 0.8928 (t) cc_final: 0.8144 (p) REVERT: D 64 ASP cc_start: 0.7964 (t0) cc_final: 0.7679 (t0) REVERT: D 98 LYS cc_start: 0.8229 (tttm) cc_final: 0.7998 (mtpp) REVERT: E 64 ASP cc_start: 0.7904 (t0) cc_final: 0.7675 (t0) REVERT: E 150 ASP cc_start: 0.8655 (t70) cc_final: 0.8349 (t70) REVERT: E 152 THR cc_start: 0.8934 (t) cc_final: 0.8189 (p) REVERT: F 64 ASP cc_start: 0.7944 (t0) cc_final: 0.7723 (t0) REVERT: F 152 THR cc_start: 0.8916 (t) cc_final: 0.8143 (p) REVERT: F 206 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7510 (pp) REVERT: H 76 MET cc_start: 0.8191 (ttp) cc_final: 0.7664 (ttt) REVERT: K 76 MET cc_start: 0.8303 (ttp) cc_final: 0.7676 (ttt) REVERT: L 120 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8034 (ttpp) outliers start: 61 outliers final: 59 residues processed: 237 average time/residue: 0.3020 time to fit residues: 102.3308 Evaluate side-chains 239 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 179 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 SER 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 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 124 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 79 ASN 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 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 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 124 THR Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain 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 35 VAL 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 152 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127838 restraints weight = 15810.446| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.19 r_work: 0.3103 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 942 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15072 Z= 0.303 Angle : 0.589 12.651 20418 Z= 0.297 Chirality : 0.049 0.140 2346 Planarity : 0.003 0.032 2568 Dihedral : 4.165 17.003 2010 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 3.77 % Allowed : 26.27 % Favored : 69.96 % 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: -0.69 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.10 (0.18), residues: 816 loop : -0.70 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 66 HIS 0.004 0.001 HIS I 130 PHE 0.006 0.001 PHE A 198 TYR 0.014 0.001 TYR G 65 ARG 0.009 0.000 ARG F 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.64 seconds wall clock time: 66 minutes 37.28 seconds (3997.28 seconds total)