Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 03:44:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg7_25106/05_2023/7sg7_25106.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.000 sd= 0.005 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 132 5.16 5 C 24696 2.51 5 N 6486 2.21 5 O 7488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 55": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 143": "OD1" <-> "OD2" Residue "T PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 168": "OD1" <-> "OD2" Residue "T PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 286": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 430": "OE1" <-> "OE2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J ASP 39": "OD1" <-> "OD2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 94": "OD1" <-> "OD2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 112": "OD1" <-> "OD2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 245": "OD1" <-> "OD2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 52": "OE1" <-> "OE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 117": "OD1" <-> "OD2" Residue "V ASP 23": "OD1" <-> "OD2" Residue "V ASP 143": "OD1" <-> "OD2" Residue "V PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 286": "OD1" <-> "OD2" Residue "V GLU 346": "OE1" <-> "OE2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ASP 117": "OD1" <-> "OD2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "M TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 112": "OD1" <-> "OD2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38802 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "B" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "T" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "S" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "U" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "K" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "V" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "G" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "L" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "W" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "X" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Time building chain proxies: 18.18, per 1000 atoms: 0.47 Number of scatterers: 38802 At special positions: 0 Unit cell: (200.838, 207.57, 126.786, 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 132 16.00 O 7488 8.00 N 6486 7.00 C 24696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 12.71 Conformation dependent library (CDL) restraints added in 5.6 seconds 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 123 sheets defined 9.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.524A pdb=" N TYR A 109 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.723A pdb=" N ASP A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 123 Proline residue: B 116 - end of helix removed outlier: 3.636A pdb=" N ALA B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.507A pdb=" N GLN C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.835A pdb=" N ASP C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 229 Processing helix chain 'T' and resid 252 through 256 Processing helix chain 'T' and resid 273 through 282 Processing helix chain 'T' and resid 318 through 320 No H-bonds generated for 'chain 'T' and resid 318 through 320' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.525A pdb=" N TYR D 109 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.792A pdb=" N ASP D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 removed outlier: 4.071A pdb=" N SER I 57 " --> pdb=" O GLU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 123 Proline residue: I 116 - end of helix Processing helix chain 'N' and resid 42 through 46 Processing helix chain 'N' and resid 54 through 56 No H-bonds generated for 'chain 'N' and resid 54 through 56' Processing helix chain 'N' and resid 113 through 124 removed outlier: 3.674A pdb=" N ASP N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 119 " --> pdb=" O GLY N 115 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 229 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.541A pdb=" N GLY S 256 " --> pdb=" O PRO S 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 282 removed outlier: 3.532A pdb=" N LYS S 278 " --> pdb=" O ALA S 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 320 No H-bonds generated for 'chain 'S' and resid 318 through 320' Processing helix chain 'E' and resid 105 through 110 removed outlier: 3.509A pdb=" N TYR E 109 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP E 110 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.757A pdb=" N ASP E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 removed outlier: 4.020A pdb=" N SER J 57 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 123 Proline residue: J 116 - end of helix removed outlier: 3.519A pdb=" N ALA J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 46 removed outlier: 3.524A pdb=" N GLN O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 123 removed outlier: 3.598A pdb=" N ASP O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 120 " --> pdb=" O PRO O 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 226 through 229 Processing helix chain 'U' and resid 252 through 256 removed outlier: 3.575A pdb=" N GLY U 256 " --> pdb=" O PRO U 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 282 removed outlier: 3.517A pdb=" N LYS U 278 " --> pdb=" O ALA U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 320 No H-bonds generated for 'chain 'U' and resid 318 through 320' Processing helix chain 'F' and resid 105 through 110 removed outlier: 3.562A pdb=" N TYR F 109 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 110 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.720A pdb=" N ASP F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 4.068A pdb=" N SER K 57 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 123 Proline residue: K 116 - end of helix Processing helix chain 'P' and resid 42 through 46 removed outlier: 3.517A pdb=" N GLN P 46 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 124 removed outlier: 3.991A pdb=" N ASP P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 118 " --> pdb=" O PHE P 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 229 Processing helix chain 'V' and resid 252 through 256 removed outlier: 3.514A pdb=" N GLY V 256 " --> pdb=" O PRO V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 282 Processing helix chain 'V' and resid 286 through 291 removed outlier: 4.168A pdb=" N ASP V 290 " --> pdb=" O GLU V 287 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY V 291 " --> pdb=" O LEU V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 318 through 320 No H-bonds generated for 'chain 'V' and resid 318 through 320' Processing helix chain 'G' and resid 105 through 110 removed outlier: 3.535A pdb=" N TYR G 109 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP G 110 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.820A pdb=" N ASP G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 57 removed outlier: 4.015A pdb=" N SER L 57 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 123 Proline residue: L 116 - end of helix Processing helix chain 'Q' and resid 42 through 46 removed outlier: 3.521A pdb=" N GLN Q 46 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 124 removed outlier: 3.895A pdb=" N ASP Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 229 Processing helix chain 'W' and resid 252 through 256 removed outlier: 3.565A pdb=" N GLY W 256 " --> pdb=" O PRO W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 282 removed outlier: 3.511A pdb=" N LYS W 278 " --> pdb=" O ALA W 274 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 320 No H-bonds generated for 'chain 'W' and resid 318 through 320' Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.532A pdb=" N TYR H 109 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP H 110 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 122 removed outlier: 3.675A pdb=" N ASP H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 57 removed outlier: 4.087A pdb=" N SER M 57 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 Proline residue: M 116 - end of helix Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 54 through 56 No H-bonds generated for 'chain 'R' and resid 54 through 56' Processing helix chain 'R' and resid 113 through 124 removed outlier: 3.827A pdb=" N ASP R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 229 Processing helix chain 'X' and resid 252 through 256 removed outlier: 3.502A pdb=" N GLY X 256 " --> pdb=" O PRO X 253 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 282 removed outlier: 3.536A pdb=" N LYS X 278 " --> pdb=" O ALA X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 320 No H-bonds generated for 'chain 'X' and resid 318 through 320' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 4.362A pdb=" N LYS C 108 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.303A pdb=" N VAL A 66 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 89 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 90 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 102 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 92 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.079A pdb=" N VAL B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 101 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 61 removed outlier: 4.780A pdb=" N VAL B 49 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS B 81 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 removed outlier: 4.680A pdb=" N VAL C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.558A pdb=" N VAL C 59 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL C 49 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'T' and resid 3 through 5 removed outlier: 6.929A pdb=" N LEU T 464 " --> pdb=" O SER T 398 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER T 398 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY T 466 " --> pdb=" O VAL T 396 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL T 396 " --> pdb=" O GLY T 466 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN T 468 " --> pdb=" O LEU T 394 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU T 394 " --> pdb=" O GLN T 468 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS T 441 " --> pdb=" O ASP T 393 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU T 395 " --> pdb=" O LEU T 439 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU T 439 " --> pdb=" O GLU T 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'T' and resid 51 through 54 removed outlier: 6.818A pdb=" N THR T 360 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 59 through 65 removed outlier: 3.555A pdb=" N GLY T 61 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU T 79 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 96 through 99 removed outlier: 3.596A pdb=" N SER T 96 " --> pdb=" O GLY T 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 141 through 147 removed outlier: 4.434A pdb=" N ASP T 143 " --> pdb=" O SER T 154 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER T 160 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 190 through 193 removed outlier: 3.503A pdb=" N GLU T 207 " --> pdb=" O CYS T 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 240 through 242 removed outlier: 5.124A pdb=" N TYR T 247 " --> pdb=" O ILE T 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 294 through 296 Processing sheet with id=AB9, first strand: chain 'T' and resid 341 through 345 removed outlier: 3.538A pdb=" N ILE T 341 " --> pdb=" O GLY T 353 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE T 343 " --> pdb=" O THR T 351 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR T 351 " --> pdb=" O PHE T 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 375 through 378 removed outlier: 3.515A pdb=" N THR T 458 " --> pdb=" O GLN T 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 384 through 385 removed outlier: 3.539A pdb=" N VAL T 450 " --> pdb=" O PHE T 384 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 8 through 9 removed outlier: 4.376A pdb=" N LYS N 108 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 78 through 79 removed outlier: 4.320A pdb=" N VAL D 66 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 89 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET D 90 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR D 102 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 92 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AC6, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.117A pdb=" N VAL I 66 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.713A pdb=" N VAL I 49 " --> pdb=" O VAL I 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'N' and resid 58 through 61 removed outlier: 4.761A pdb=" N VAL N 49 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AD2, first strand: chain 'S' and resid 3 through 5 Processing sheet with id=AD3, first strand: chain 'S' and resid 3 through 5 removed outlier: 6.907A pdb=" N LEU S 464 " --> pdb=" O SER S 398 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER S 398 " --> pdb=" O LEU S 464 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY S 466 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL S 396 " --> pdb=" O GLY S 466 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN S 468 " --> pdb=" O LEU S 394 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU S 394 " --> pdb=" O GLN S 468 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS S 441 " --> pdb=" O ASP S 393 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU S 395 " --> pdb=" O LEU S 439 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU S 439 " --> pdb=" O GLU S 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 11 through 14 Processing sheet with id=AD5, first strand: chain 'S' and resid 51 through 54 removed outlier: 6.833A pdb=" N THR S 360 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 59 through 65 removed outlier: 3.638A pdb=" N GLY S 61 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU S 79 " --> pdb=" O VAL S 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 99 removed outlier: 3.936A pdb=" N SER S 96 " --> pdb=" O GLY S 107 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 141 through 143 removed outlier: 6.976A pdb=" N SER S 154 " --> pdb=" O ARG S 142 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 190 through 193 Processing sheet with id=AE1, first strand: chain 'S' and resid 240 through 242 removed outlier: 5.212A pdb=" N TYR S 247 " --> pdb=" O ILE S 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 295 through 296 removed outlier: 3.553A pdb=" N LEU S 296 " --> pdb=" O LEU S 303 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 344 through 346 Processing sheet with id=AE4, first strand: chain 'S' and resid 384 through 385 Processing sheet with id=AE5, first strand: chain 'S' and resid 408 through 411 Processing sheet with id=AE6, first strand: chain 'E' and resid 8 through 9 removed outlier: 4.367A pdb=" N LYS O 108 " --> pdb=" O VAL E 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 78 through 79 removed outlier: 4.330A pdb=" N VAL E 66 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 29 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET E 90 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR E 102 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 92 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 58 through 61 removed outlier: 4.851A pdb=" N VAL E 49 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 73 through 74 removed outlier: 4.154A pdb=" N VAL J 66 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 59 through 61 removed outlier: 4.502A pdb=" N VAL J 49 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 30 through 31 removed outlier: 4.660A pdb=" N VAL O 66 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 58 through 61 removed outlier: 4.810A pdb=" N VAL O 49 " --> pdb=" O VAL O 61 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'U' and resid 3 through 5 removed outlier: 6.925A pdb=" N LEU U 464 " --> pdb=" O SER U 398 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER U 398 " --> pdb=" O LEU U 464 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLY U 466 " --> pdb=" O VAL U 396 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL U 396 " --> pdb=" O GLY U 466 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN U 468 " --> pdb=" O LEU U 394 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU U 394 " --> pdb=" O GLN U 468 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS U 441 " --> pdb=" O ASP U 393 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU U 395 " --> pdb=" O LEU U 439 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU U 439 " --> pdb=" O GLU U 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 11 through 15 removed outlier: 3.634A pdb=" N ASP U 20 " --> pdb=" O ASP U 15 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 51 through 54 removed outlier: 6.783A pdb=" N THR U 360 " --> pdb=" O ARG U 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 59 through 65 removed outlier: 3.569A pdb=" N GLY U 61 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU U 79 " --> pdb=" O VAL U 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 96 through 99 removed outlier: 3.621A pdb=" N SER U 96 " --> pdb=" O GLY U 107 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 141 through 143 removed outlier: 6.967A pdb=" N SER U 154 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 146 through 147 Processing sheet with id=AG3, first strand: chain 'U' and resid 188 through 193 Processing sheet with id=AG4, first strand: chain 'U' and resid 240 through 242 removed outlier: 5.184A pdb=" N TYR U 247 " --> pdb=" O ILE U 263 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 294 through 296 removed outlier: 3.540A pdb=" N LEU U 296 " --> pdb=" O LEU U 303 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 344 through 346 Processing sheet with id=AG7, first strand: chain 'U' and resid 384 through 385 Processing sheet with id=AG8, first strand: chain 'U' and resid 410 through 411 Processing sheet with id=AG9, first strand: chain 'F' and resid 78 through 79 removed outlier: 4.290A pdb=" N VAL F 66 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET F 90 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR F 102 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F 92 " --> pdb=" O GLN F 100 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 58 through 60 Processing sheet with id=AH2, first strand: chain 'K' and resid 73 through 74 removed outlier: 4.086A pdb=" N VAL K 66 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 59 through 61 removed outlier: 4.601A pdb=" N VAL K 49 " --> pdb=" O VAL K 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 30 through 31 removed outlier: 4.680A pdb=" N VAL P 66 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR P 72 " --> pdb=" O ASN P 68 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 58 through 61 removed outlier: 3.541A pdb=" N VAL P 59 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL P 49 " --> pdb=" O VAL P 61 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'V' and resid 3 through 5 Processing sheet with id=AH7, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.929A pdb=" N LEU V 464 " --> pdb=" O SER V 398 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER V 398 " --> pdb=" O LEU V 464 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY V 466 " --> pdb=" O VAL V 396 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL V 396 " --> pdb=" O GLY V 466 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN V 468 " --> pdb=" O LEU V 394 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU V 394 " --> pdb=" O GLN V 468 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS V 441 " --> pdb=" O ASP V 393 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU V 395 " --> pdb=" O LEU V 439 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU V 439 " --> pdb=" O GLU V 395 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'V' and resid 51 through 54 removed outlier: 6.820A pdb=" N THR V 360 " --> pdb=" O ARG V 52 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 59 through 65 removed outlier: 3.555A pdb=" N GLY V 61 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU V 79 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 96 through 99 removed outlier: 3.623A pdb=" N SER V 96 " --> pdb=" O GLY V 107 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 141 through 143 removed outlier: 6.977A pdb=" N SER V 154 " --> pdb=" O ARG V 142 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 160 through 161 Processing sheet with id=AI5, first strand: chain 'V' and resid 190 through 193 Processing sheet with id=AI6, first strand: chain 'V' and resid 240 through 242 removed outlier: 5.124A pdb=" N TYR V 247 " --> pdb=" O ILE V 263 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 294 through 296 Processing sheet with id=AI8, first strand: chain 'V' and resid 343 through 346 Processing sheet with id=AI9, first strand: chain 'V' and resid 384 through 385 Processing sheet with id=AJ1, first strand: chain 'V' and resid 424 through 425 Processing sheet with id=AJ2, first strand: chain 'G' and resid 78 through 79 removed outlier: 4.302A pdb=" N VAL G 66 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY G 29 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET G 90 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR G 102 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL G 92 " --> pdb=" O GLN G 100 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 58 through 61 removed outlier: 4.854A pdb=" N VAL G 49 " --> pdb=" O VAL G 61 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 73 through 74 removed outlier: 4.099A pdb=" N VAL L 66 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 59 through 61 removed outlier: 4.526A pdb=" N VAL L 49 " --> pdb=" O VAL L 61 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 30 through 31 removed outlier: 4.662A pdb=" N VAL Q 66 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR Q 72 " --> pdb=" O ASN Q 68 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 58 through 61 removed outlier: 4.821A pdb=" N VAL Q 49 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'W' and resid 3 through 5 Processing sheet with id=AJ9, first strand: chain 'W' and resid 3 through 5 removed outlier: 6.926A pdb=" N LEU W 464 " --> pdb=" O SER W 398 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER W 398 " --> pdb=" O LEU W 464 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY W 466 " --> pdb=" O VAL W 396 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL W 396 " --> pdb=" O GLY W 466 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN W 468 " --> pdb=" O LEU W 394 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU W 394 " --> pdb=" O GLN W 468 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS W 441 " --> pdb=" O ASP W 393 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU W 395 " --> pdb=" O LEU W 439 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU W 439 " --> pdb=" O GLU W 395 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'W' and resid 11 through 14 Processing sheet with id=AK2, first strand: chain 'W' and resid 51 through 54 removed outlier: 6.781A pdb=" N THR W 360 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'W' and resid 59 through 65 removed outlier: 3.546A pdb=" N GLY W 61 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU W 79 " --> pdb=" O VAL W 86 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'W' and resid 96 through 99 removed outlier: 3.696A pdb=" N SER W 96 " --> pdb=" O GLY W 107 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'W' and resid 141 through 143 removed outlier: 6.970A pdb=" N SER W 154 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'W' and resid 146 through 147 Processing sheet with id=AK7, first strand: chain 'W' and resid 190 through 193 Processing sheet with id=AK8, first strand: chain 'W' and resid 240 through 242 removed outlier: 5.207A pdb=" N TYR W 247 " --> pdb=" O ILE W 263 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'W' and resid 294 through 296 Processing sheet with id=AL1, first strand: chain 'W' and resid 343 through 346 Processing sheet with id=AL2, first strand: chain 'W' and resid 375 through 378 removed outlier: 3.566A pdb=" N GLN W 375 " --> pdb=" O THR W 458 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR W 458 " --> pdb=" O GLN W 375 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'W' and resid 384 through 385 Processing sheet with id=AL4, first strand: chain 'W' and resid 410 through 411 Processing sheet with id=AL5, first strand: chain 'H' and resid 78 through 79 removed outlier: 4.310A pdb=" N VAL H 66 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET H 90 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 102 " --> pdb=" O MET H 90 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL H 92 " --> pdb=" O GLN H 100 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AL7, first strand: chain 'M' and resid 73 through 74 removed outlier: 4.091A pdb=" N VAL M 66 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 59 through 61 removed outlier: 4.712A pdb=" N VAL M 49 " --> pdb=" O VAL M 61 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AM1, first strand: chain 'R' and resid 58 through 61 removed outlier: 4.765A pdb=" N VAL R 49 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AM3, first strand: chain 'X' and resid 3 through 5 Processing sheet with id=AM4, first strand: chain 'X' and resid 3 through 5 removed outlier: 6.905A pdb=" N LEU X 464 " --> pdb=" O SER X 398 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER X 398 " --> pdb=" O LEU X 464 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY X 466 " --> pdb=" O VAL X 396 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL X 396 " --> pdb=" O GLY X 466 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN X 468 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU X 394 " --> pdb=" O GLN X 468 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS X 441 " --> pdb=" O ASP X 393 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU X 395 " --> pdb=" O LEU X 439 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU X 439 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AM6, first strand: chain 'X' and resid 51 through 54 removed outlier: 6.835A pdb=" N THR X 360 " --> pdb=" O ARG X 52 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'X' and resid 59 through 65 removed outlier: 3.633A pdb=" N GLY X 61 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU X 79 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'X' and resid 96 through 99 removed outlier: 3.544A pdb=" N SER X 96 " --> pdb=" O GLY X 107 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'X' and resid 141 through 143 removed outlier: 6.973A pdb=" N SER X 154 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'X' and resid 188 through 193 Processing sheet with id=AN2, first strand: chain 'X' and resid 240 through 242 removed outlier: 5.218A pdb=" N TYR X 247 " --> pdb=" O ILE X 263 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'X' and resid 295 through 296 removed outlier: 3.535A pdb=" N LEU X 296 " --> pdb=" O LEU X 303 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'X' and resid 344 through 345 Processing sheet with id=AN5, first strand: chain 'X' and resid 384 through 385 Processing sheet with id=AN6, first strand: chain 'X' and resid 410 through 411 906 hydrogen bonds defined for protein. 2163 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: 16.15 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6606 1.30 - 1.43: 10524 1.43 - 1.56: 22331 1.56 - 1.68: 1 1.68 - 1.81: 228 Bond restraints: 39690 Sorted by residual: bond pdb=" C PRO W 382 " pdb=" O PRO W 382 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C PRO U 382 " pdb=" O PRO U 382 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C PRO V 382 " pdb=" O PRO V 382 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.23e-02 6.61e+03 1.20e+01 bond pdb=" C PRO T 382 " pdb=" O PRO T 382 " ideal model delta sigma weight residual 1.233 1.192 0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" N ILE T 144 " pdb=" CA ILE T 144 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 ... (remaining 39685 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.33: 1161 106.33 - 113.39: 20657 113.39 - 120.44: 14971 120.44 - 127.49: 16781 127.49 - 134.54: 352 Bond angle restraints: 53922 Sorted by residual: angle pdb=" N ASP T 130 " pdb=" CA ASP T 130 " pdb=" C ASP T 130 " ideal model delta sigma weight residual 113.16 104.21 8.95 1.24e+00 6.50e-01 5.20e+01 angle pdb=" C ASN R 7 " pdb=" CA ASN R 7 " pdb=" CB ASN R 7 " ideal model delta sigma weight residual 117.23 109.83 7.40 1.36e+00 5.41e-01 2.96e+01 angle pdb=" C GLY T 372 " pdb=" N LEU T 373 " pdb=" CA LEU T 373 " ideal model delta sigma weight residual 122.93 115.21 7.72 1.45e+00 4.76e-01 2.84e+01 angle pdb=" C ILE T 426 " pdb=" N GLU T 427 " pdb=" CA GLU T 427 " ideal model delta sigma weight residual 122.19 133.93 -11.74 2.30e+00 1.89e-01 2.60e+01 angle pdb=" C ILE V 426 " pdb=" N GLU V 427 " pdb=" CA GLU V 427 " ideal model delta sigma weight residual 122.19 133.83 -11.64 2.30e+00 1.89e-01 2.56e+01 ... (remaining 53917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 21341 17.80 - 35.61: 1727 35.61 - 53.41: 308 53.41 - 71.21: 91 71.21 - 89.01: 53 Dihedral angle restraints: 23520 sinusoidal: 9174 harmonic: 14346 Sorted by residual: dihedral pdb=" CA GLY I 87 " pdb=" C GLY I 87 " pdb=" N HIS I 88 " pdb=" CA HIS I 88 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLY K 87 " pdb=" C GLY K 87 " pdb=" N HIS K 88 " pdb=" CA HIS K 88 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY M 87 " pdb=" C GLY M 87 " pdb=" N HIS M 88 " pdb=" CA HIS M 88 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 23517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4513 0.059 - 0.118: 1165 0.118 - 0.176: 154 0.176 - 0.235: 27 0.235 - 0.294: 9 Chirality restraints: 5868 Sorted by residual: chirality pdb=" CA GLU W 376 " pdb=" N GLU W 376 " pdb=" C GLU W 376 " pdb=" CB GLU W 376 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ILE S 426 " pdb=" N ILE S 426 " pdb=" C ILE S 426 " pdb=" CB ILE S 426 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA THR G 6 " pdb=" N THR G 6 " pdb=" C THR G 6 " pdb=" CB THR G 6 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 5865 not shown) Planarity restraints: 7104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN W 374 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C GLN W 374 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN W 374 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN W 375 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 379 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C LEU U 379 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU U 379 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE U 380 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG T 150 " 0.017 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C ARG T 150 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG T 150 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR T 151 " 0.022 2.00e-02 2.50e+03 ... (remaining 7101 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 500 2.65 - 3.22: 33799 3.22 - 3.78: 54077 3.78 - 4.34: 79163 4.34 - 4.90: 135688 Nonbonded interactions: 303227 Sorted by model distance: nonbonded pdb=" OD1 ASP N 94 " pdb=" N ALA N 95 " model vdw 2.092 2.520 nonbonded pdb=" O ALA Q 27 " pdb=" ND2 ASN Q 28 " model vdw 2.124 2.520 nonbonded pdb=" OD2 ASP W 186 " pdb=" OG SER W 203 " model vdw 2.128 2.440 nonbonded pdb=" OD1 ASP L 94 " pdb=" N ALA L 95 " model vdw 2.130 2.520 nonbonded pdb=" OD1 ASP K 94 " pdb=" N ALA K 95 " model vdw 2.136 2.520 ... (remaining 303222 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' and resid 7 through 123) selection = chain 'B' selection = (chain 'C' and resid 7 through 123) selection = (chain 'D' and resid 7 through 123) selection = (chain 'E' and resid 7 through 123) selection = (chain 'F' and resid 7 through 123) selection = (chain 'G' and resid 7 through 123) selection = (chain 'H' and resid 7 through 123) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 7 through 123) selection = (chain 'O' and resid 7 through 123) selection = (chain 'P' and resid 7 through 123) selection = (chain 'Q' and resid 7 through 123) selection = (chain 'R' and resid 7 through 123) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=1.00 max=1.00 mean=1.00 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: 7.960 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: 0.040 Extract box with map and model: 31.010 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 88.510 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.004 0.071 39690 Z= 0.241 Angle : 0.652 11.736 53922 Z= 0.388 Chirality : 0.053 0.294 5868 Planarity : 0.004 0.086 7104 Dihedral : 14.503 89.015 14424 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 4926 helix: -0.68 (0.32), residues: 252 sheet: -1.20 (0.14), residues: 1368 loop : -1.51 (0.10), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 590 time to evaluate : 4.603 Fit side-chains outliers start: 29 outliers final: 5 residues processed: 613 average time/residue: 1.4767 time to fit residues: 1109.9304 Evaluate side-chains 515 residues out of total 4176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 510 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.3186 time to fit residues: 6.6884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: