Starting phenix.real_space_refine on Thu Mar 21 23:28:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frs_29406/03_2024/8frs_29406.pdb" } resolution = 3.96 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= -0.000 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 78 5.16 5 C 19970 2.51 5 N 5370 2.21 5 O 6079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 165": "OE1" <-> "OE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g GLU 115": "OE1" <-> "OE2" Residue "h GLU 64": "OE1" <-> "OE2" Residue "h GLU 117": "OE1" <-> "OE2" Residue "h ASP 120": "OD1" <-> "OD2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H GLU 359": "OE1" <-> "OE2" Residue "H TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 101": "OD1" <-> "OD2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I GLU 177": "OE1" <-> "OE2" Residue "J TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J ASP 328": "OD1" <-> "OD2" Residue "K ASP 101": "OD1" <-> "OD2" Residue "K ASP 107": "OD1" <-> "OD2" Residue "K GLU 177": "OE1" <-> "OE2" Residue "K TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 285": "OD1" <-> "OD2" Residue "K ASP 328": "OD1" <-> "OD2" Residue "K TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31497 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "E" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "F" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "f" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "g" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "h" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "G" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "I" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "J" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "K" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Time building chain proxies: 16.07, per 1000 atoms: 0.51 Number of scatterers: 31497 At special positions: 0 Unit cell: (281.12, 247.52, 137.76, 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 78 16.00 O 6079 8.00 N 5370 7.00 C 19970 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: 11.69 Conformation dependent library (CDL) restraints added in 5.7 seconds 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7462 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 57 sheets defined 24.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.814A pdb=" N ILE B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 197 Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.692A pdb=" N ILE B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.815A pdb=" N GLU B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.901A pdb=" N LEU B 302 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.976A pdb=" N ILE A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.535A pdb=" N GLY A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.509A pdb=" N ALA A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.729A pdb=" N GLU A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 removed outlier: 5.200A pdb=" N ASP A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 272 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 273 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 274 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 275 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.538A pdb=" N LEU A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.546A pdb=" N ILE C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.764A pdb=" N GLY C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 174 through 197 removed outlier: 3.546A pdb=" N ALA C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 250 removed outlier: 3.595A pdb=" N ASP C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.189A pdb=" N GLU C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.572A pdb=" N SER C 274 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.765A pdb=" N ILE D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.673A pdb=" N GLY D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 174 through 197 removed outlier: 3.528A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.556A pdb=" N ILE D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.096A pdb=" N GLU D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.577A pdb=" N TRP D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.521A pdb=" N SER D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.702A pdb=" N ILE E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 169 Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 174 through 197 removed outlier: 3.532A pdb=" N ALA E 184 " --> pdb=" O ARG E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 250 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.645A pdb=" N GLU E 259 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 275 removed outlier: 3.567A pdb=" N VAL E 270 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP E 271 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 273 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 274 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 299 through 303 removed outlier: 3.741A pdb=" N LEU E 302 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.716A pdb=" N ILE F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 removed outlier: 3.579A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 174 through 197 Processing helix chain 'F' and resid 231 through 250 removed outlier: 3.675A pdb=" N ILE F 239 " --> pdb=" O ILE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.040A pdb=" N GLU F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.602A pdb=" N LEU F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 274 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.549A pdb=" N TRP F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'f' and resid 33 through 37 Processing helix chain 'f' and resid 90 through 94 removed outlier: 3.588A pdb=" N TYR f 94 " --> pdb=" O PRO f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 37 Processing helix chain 'g' and resid 90 through 94 Processing helix chain 'g' and resid 153 through 157 Processing helix chain 'h' and resid 33 through 37 Processing helix chain 'h' and resid 90 through 94 Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 162 through 171 removed outlier: 3.677A pdb=" N ALA H 170 " --> pdb=" O GLY H 166 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 197 Processing helix chain 'H' and resid 231 through 250 Processing helix chain 'H' and resid 269 through 275 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 372 through 374 No H-bonds generated for 'chain 'H' and resid 372 through 374' Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 162 through 171 removed outlier: 3.519A pdb=" N ALA G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 197 Processing helix chain 'G' and resid 231 through 250 removed outlier: 3.673A pdb=" N ILE G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 Processing helix chain 'G' and resid 282 through 291 Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 372 through 374 No H-bonds generated for 'chain 'G' and resid 372 through 374' Processing helix chain 'I' and resid 99 through 104 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.639A pdb=" N ALA I 170 " --> pdb=" O GLY I 166 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 197 Processing helix chain 'I' and resid 231 through 250 removed outlier: 3.645A pdb=" N ILE I 239 " --> pdb=" O ILE I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 275 Processing helix chain 'I' and resid 282 through 291 Processing helix chain 'I' and resid 299 through 303 Processing helix chain 'I' and resid 372 through 374 No H-bonds generated for 'chain 'I' and resid 372 through 374' Processing helix chain 'J' and resid 99 through 104 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.593A pdb=" N ALA J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 197 Processing helix chain 'J' and resid 231 through 250 removed outlier: 3.659A pdb=" N ILE J 239 " --> pdb=" O ILE J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 275 Processing helix chain 'J' and resid 282 through 291 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 372 through 374 No H-bonds generated for 'chain 'J' and resid 372 through 374' Processing helix chain 'K' and resid 99 through 105 removed outlier: 3.772A pdb=" N ILE K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 169 Processing helix chain 'K' and resid 170 through 172 No H-bonds generated for 'chain 'K' and resid 170 through 172' Processing helix chain 'K' and resid 174 through 197 Processing helix chain 'K' and resid 231 through 250 removed outlier: 3.512A pdb=" N ASP K 238 " --> pdb=" O GLY K 234 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE K 239 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 275 Processing helix chain 'K' and resid 282 through 291 Processing helix chain 'K' and resid 299 through 303 Processing helix chain 'K' and resid 372 through 374 No H-bonds generated for 'chain 'K' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'B' and resid 84 through 86 removed outlier: 3.552A pdb=" N ILE F 117 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 145 " --> pdb=" O ILE F 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 108 removed outlier: 5.875A pdb=" N ASP B 107 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER B 343 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N GLN B 339 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N CYS B 370 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N VAL B 341 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N ALA B 368 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N SER B 343 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA B 366 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE B 345 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLY B 364 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR B 347 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 362 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 349 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 150 removed outlier: 13.047A pdb=" N GLU B 116 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 13.729A pdb=" N GLY A 89 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL B 118 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N VAL A 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY B 120 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.503A pdb=" N VAL A 160 " --> pdb=" O TYR A 357 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 357 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 349 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 362 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR A 347 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY A 364 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE A 345 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA7, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.437A pdb=" N GLU A 116 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 87 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 118 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY C 89 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY A 120 " --> pdb=" O GLY C 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.526A pdb=" N VAL C 160 " --> pdb=" O TYR C 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 357 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY C 349 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 362 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR C 347 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY C 364 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE C 345 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA C 366 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N SER C 343 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA C 368 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N VAL C 341 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N CYS C 370 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N GLN C 339 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP C 107 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER C 343 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.654A pdb=" N GLY A 367 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.669A pdb=" N ILE C 117 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C 116 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 126 removed outlier: 3.524A pdb=" N SER C 141 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.513A pdb=" N VAL D 160 " --> pdb=" O TYR D 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 357 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY D 349 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 362 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR D 347 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLY D 364 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE D 345 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA D 366 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N SER D 343 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ALA D 368 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N VAL D 341 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N CYS D 370 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N GLN D 339 " --> pdb=" O CYS D 370 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP D 107 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER D 343 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB7, first strand: chain 'D' and resid 145 through 150 removed outlier: 6.611A pdb=" N GLU D 116 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU E 87 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 118 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 89 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY D 120 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB9, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.570A pdb=" N VAL E 160 " --> pdb=" O TYR E 357 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 357 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N SER E 356 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL E 350 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL E 358 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU E 348 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP E 360 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE E 346 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER E 362 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS E 344 " --> pdb=" O SER E 362 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY E 364 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU E 340 " --> pdb=" O ALA E 366 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA E 368 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 338 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP E 107 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER E 343 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AC2, first strand: chain 'E' and resid 145 through 150 removed outlier: 6.551A pdb=" N GLU E 116 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU F 87 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL E 118 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY F 89 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY E 120 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 130 removed outlier: 11.473A pdb=" N SER F 356 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL F 350 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL F 358 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU F 348 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP F 360 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE F 346 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER F 362 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS F 344 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY F 364 " --> pdb=" O GLN F 342 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU F 340 " --> pdb=" O ALA F 366 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA F 368 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER F 338 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.077A pdb=" N ILE E 137 " --> pdb=" O ASP h 21 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY h 124 " --> pdb=" O ILE h 19 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 295 through 296 Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AC8, first strand: chain 'F' and resid 295 through 296 Processing sheet with id=AC9, first strand: chain 'f' and resid 25 through 31 removed outlier: 10.951A pdb=" N SER f 75 " --> pdb=" O ALA f 26 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL f 77 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG f 30 " --> pdb=" O VAL f 77 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU f 76 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE f 53 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 12.420A pdb=" N PHE f 85 " --> pdb=" O MET f 121 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET f 121 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLU f 115 " --> pdb=" O ILE f 31 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE f 31 " --> pdb=" O GLU f 115 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU f 117 " --> pdb=" O GLY f 29 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY f 29 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE f 119 " --> pdb=" O ARG f 27 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG f 27 " --> pdb=" O PHE f 119 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 179 through 180 removed outlier: 4.278A pdb=" N LEU f 166 " --> pdb=" O GLU f 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY f 168 " --> pdb=" O PHE f 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 137 through 138 Processing sheet with id=AD3, first strand: chain 'g' and resid 205 through 208 removed outlier: 7.628A pdb=" N MET g 121 " --> pdb=" O PHE g 85 " (cutoff:3.500A) removed outlier: 12.440A pdb=" N PHE g 85 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE g 53 " --> pdb=" O PHE g 85 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU g 76 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N SER g 75 " --> pdb=" O ALA g 26 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL g 77 " --> pdb=" O PRO g 28 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG g 30 " --> pdb=" O VAL g 77 " (cutoff:3.500A) removed outlier: 10.786A pdb=" N ASP g 17 " --> pdb=" O GLU g 128 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU g 128 " --> pdb=" O ASP g 17 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE g 19 " --> pdb=" O VAL g 126 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL g 126 " --> pdb=" O ILE g 19 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP g 21 " --> pdb=" O GLY g 124 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY g 124 " --> pdb=" O ASP g 21 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA g 122 " --> pdb=" O PRO g 23 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG g 25 " --> pdb=" O ASP g 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 137 through 138 Processing sheet with id=AD5, first strand: chain 'g' and resid 166 through 169 Processing sheet with id=AD6, first strand: chain 'h' and resid 25 through 31 removed outlier: 11.271A pdb=" N SER h 75 " --> pdb=" O ALA h 26 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL h 77 " --> pdb=" O PRO h 28 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG h 30 " --> pdb=" O VAL h 77 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU h 76 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE h 53 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 12.487A pdb=" N PHE h 85 " --> pdb=" O MET h 121 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N MET h 121 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU h 115 " --> pdb=" O ILE h 31 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE h 31 " --> pdb=" O GLU h 115 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU h 117 " --> pdb=" O GLY h 29 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY h 29 " --> pdb=" O GLU h 117 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE h 119 " --> pdb=" O ARG h 27 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG h 27 " --> pdb=" O PHE h 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 179 through 180 removed outlier: 4.665A pdb=" N LEU h 166 " --> pdb=" O GLU h 128 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY h 168 " --> pdb=" O PHE h 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'h' and resid 137 through 138 Processing sheet with id=AD9, first strand: chain 'H' and resid 84 through 91 removed outlier: 3.529A pdb=" N THR H 85 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY G 120 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 89 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 145 through 150 removed outlier: 13.229A pdb=" N GLU H 116 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N GLY K 89 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL H 118 " --> pdb=" O GLY K 89 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N VAL K 91 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY H 120 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 124 through 125 Processing sheet with id=AE3, first strand: chain 'H' and resid 152 through 161 removed outlier: 11.752A pdb=" N SER H 356 " --> pdb=" O VAL H 350 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N VAL H 350 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N VAL H 358 " --> pdb=" O LEU H 348 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N LEU H 348 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP H 360 " --> pdb=" O ILE H 346 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE H 346 " --> pdb=" O ASP H 360 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER H 362 " --> pdb=" O LYS H 344 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS H 344 " --> pdb=" O SER H 362 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY H 364 " --> pdb=" O GLN H 342 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU H 340 " --> pdb=" O ALA H 366 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 368 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER H 338 " --> pdb=" O ALA H 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 86 removed outlier: 6.930A pdb=" N THR G 85 " --> pdb=" O VAL I 118 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N GLY I 120 " --> pdb=" O THR G 85 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 124 through 125 Processing sheet with id=AE7, first strand: chain 'G' and resid 152 through 161 removed outlier: 11.678A pdb=" N SER G 356 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N VAL G 350 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N VAL G 358 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU G 348 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASP G 360 " --> pdb=" O ILE G 346 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE G 346 " --> pdb=" O ASP G 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER G 362 " --> pdb=" O LYS G 344 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS G 344 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY G 364 " --> pdb=" O GLN G 342 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU G 340 " --> pdb=" O ALA G 366 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA G 368 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER G 338 " --> pdb=" O ALA G 368 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 295 through 296 removed outlier: 3.554A pdb=" N LEU G 316 " --> pdb=" O TYR G 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 84 through 91 removed outlier: 3.528A pdb=" N THR I 85 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY J 120 " --> pdb=" O LEU I 87 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY I 89 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AF2, first strand: chain 'I' and resid 152 through 161 removed outlier: 3.516A pdb=" N ASP I 360 " --> pdb=" O GLY I 349 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY I 349 " --> pdb=" O ASP I 360 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER I 362 " --> pdb=" O THR I 347 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR I 347 " --> pdb=" O SER I 362 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLY I 364 " --> pdb=" O PHE I 345 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE I 345 " --> pdb=" O GLY I 364 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 295 through 296 Processing sheet with id=AF4, first strand: chain 'I' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'J' and resid 84 through 91 removed outlier: 6.244A pdb=" N GLY K 120 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY J 89 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 124 through 125 Processing sheet with id=AF7, first strand: chain 'J' and resid 152 through 161 removed outlier: 3.574A pdb=" N ASP J 360 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY J 349 " --> pdb=" O ASP J 360 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER J 362 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR J 347 " --> pdb=" O SER J 362 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY J 364 " --> pdb=" O PHE J 345 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE J 345 " --> pdb=" O GLY J 364 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 295 through 296 Processing sheet with id=AF9, first strand: chain 'J' and resid 337 through 340 removed outlier: 3.866A pdb=" N GLY J 367 " --> pdb=" O LEU J 340 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AG2, first strand: chain 'K' and resid 152 through 161 removed outlier: 11.652A pdb=" N SER K 356 " --> pdb=" O VAL K 350 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N VAL K 350 " --> pdb=" O SER K 356 " (cutoff:3.500A) removed outlier: 11.666A pdb=" N VAL K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU K 348 " --> pdb=" O VAL K 358 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP K 360 " --> pdb=" O ILE K 346 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE K 346 " --> pdb=" O ASP K 360 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER K 362 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS K 344 " --> pdb=" O SER K 362 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY K 364 " --> pdb=" O GLN K 342 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU K 340 " --> pdb=" O ALA K 366 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA K 368 " --> pdb=" O SER K 338 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER K 338 " --> pdb=" O ALA K 368 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 295 through 296 976 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.89 Time building geometry restraints manager: 12.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10513 1.34 - 1.46: 6865 1.46 - 1.58: 14656 1.58 - 1.70: 0 1.70 - 1.81: 145 Bond restraints: 32179 Sorted by residual: bond pdb=" C ASN g 38 " pdb=" N PRO g 39 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.60e+00 bond pdb=" C ASN h 38 " pdb=" N PRO h 39 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.57e+00 bond pdb=" C ALA K 125 " pdb=" N GLY K 126 " ideal model delta sigma weight residual 1.319 1.335 -0.016 1.34e-02 5.57e+03 1.40e+00 bond pdb=" C ALA J 125 " pdb=" N GLY J 126 " ideal model delta sigma weight residual 1.319 1.334 -0.015 1.34e-02 5.57e+03 1.32e+00 bond pdb=" C ALA I 125 " pdb=" N GLY I 126 " ideal model delta sigma weight residual 1.319 1.334 -0.015 1.34e-02 5.57e+03 1.31e+00 ... (remaining 32174 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.92: 712 104.92 - 112.20: 16087 112.20 - 119.48: 10516 119.48 - 126.75: 15924 126.75 - 134.03: 590 Bond angle restraints: 43829 Sorted by residual: angle pdb=" C MET G 94 " pdb=" N THR G 95 " pdb=" CA THR G 95 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C MET K 94 " pdb=" N THR K 95 " pdb=" CA THR K 95 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C MET A 94 " pdb=" N THR A 95 " pdb=" CA THR A 95 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL J 129 " pdb=" CA VAL J 129 " pdb=" C VAL J 129 " ideal model delta sigma weight residual 113.20 110.02 3.18 9.60e-01 1.09e+00 1.09e+01 angle pdb=" C MET E 94 " pdb=" N THR E 95 " pdb=" CA THR E 95 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 ... (remaining 43824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17419 17.95 - 35.91: 1309 35.91 - 53.86: 239 53.86 - 71.82: 69 71.82 - 89.77: 61 Dihedral angle restraints: 19097 sinusoidal: 7420 harmonic: 11677 Sorted by residual: dihedral pdb=" CA VAL J 93 " pdb=" C VAL J 93 " pdb=" N MET J 94 " pdb=" CA MET J 94 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LYS J 308 " pdb=" C LYS J 308 " pdb=" N ASN J 309 " pdb=" CA ASN J 309 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS K 308 " pdb=" C LYS K 308 " pdb=" N ASN K 309 " pdb=" CA ASN K 309 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 19094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3259 0.033 - 0.066: 1074 0.066 - 0.098: 298 0.098 - 0.131: 281 0.131 - 0.164: 26 Chirality restraints: 4938 Sorted by residual: chirality pdb=" CA ILE A 121 " pdb=" N ILE A 121 " pdb=" C ILE A 121 " pdb=" CB ILE A 121 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE G 117 " pdb=" N ILE G 117 " pdb=" C ILE G 117 " pdb=" CB ILE G 117 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE K 117 " pdb=" N ILE K 117 " pdb=" C ILE K 117 " pdb=" CB ILE K 117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 4935 not shown) Planarity restraints: 5745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL h 148 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO h 149 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO h 149 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO h 149 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL g 148 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO g 149 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO g 149 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO g 149 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 216 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO F 217 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 217 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 217 " 0.024 5.00e-02 4.00e+02 ... (remaining 5742 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3078 2.75 - 3.28: 30146 3.28 - 3.82: 47895 3.82 - 4.36: 57255 4.36 - 4.90: 101486 Nonbonded interactions: 239860 Sorted by model distance: nonbonded pdb=" O MET I 94 " pdb=" OG1 THR I 95 " model vdw 2.208 2.440 nonbonded pdb=" OD2 ASP D 252 " pdb=" OG1 THR E 267 " model vdw 2.226 2.440 nonbonded pdb=" O MET H 94 " pdb=" OG1 THR H 95 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR h 42 " pdb=" O LEU h 152 " model vdw 2.251 2.440 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 2.440 ... (remaining 239855 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'f' selection = chain 'g' selection = chain 'h' } 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 group one per residue 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: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 28.920 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 76.350 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.230 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.002 0.026 32179 Z= 0.140 Angle : 0.539 8.787 43829 Z= 0.299 Chirality : 0.043 0.164 4938 Planarity : 0.004 0.064 5745 Dihedral : 14.450 89.770 11635 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.11 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4092 helix: 0.34 (0.18), residues: 852 sheet: -0.34 (0.17), residues: 1031 loop : -2.18 (0.11), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 232 HIS 0.002 0.000 HIS f 93 PHE 0.009 0.001 PHE I 219 TYR 0.027 0.001 TYR H 279 ARG 0.004 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.508 Fit side-chains revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7956 (m-30) cc_final: 0.7550 (m-30) REVERT: D 159 MET cc_start: 0.8812 (ttm) cc_final: 0.8527 (ttt) REVERT: E 101 ASP cc_start: 0.8619 (m-30) cc_final: 0.8359 (m-30) REVERT: E 307 MET cc_start: 0.7926 (tpt) cc_final: 0.6719 (mtt) REVERT: F 94 MET cc_start: 0.8332 (tpt) cc_final: 0.8072 (tpt) REVERT: F 321 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6999 (mt-10) REVERT: H 279 TYR cc_start: 0.8042 (m-80) cc_final: 0.6730 (t80) REVERT: H 382 ILE cc_start: 0.6633 (mt) cc_final: 0.6343 (mt) REVERT: G 279 TYR cc_start: 0.8433 (m-80) cc_final: 0.8175 (m-80) REVERT: J 279 TYR cc_start: 0.8132 (m-80) cc_final: 0.7912 (m-80) REVERT: K 123 GLU cc_start: 0.8243 (tp30) cc_final: 0.7358 (mt-10) REVERT: K 279 TYR cc_start: 0.8322 (m-80) cc_final: 0.7044 (m-10) REVERT: K 382 ILE cc_start: 0.6562 (mt) cc_final: 0.6246 (mt) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.4044 time to fit residues: 228.0244 Evaluate side-chains 293 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 199 ASN h 38 ASN ** h 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN I 119 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32179 Z= 0.286 Angle : 0.592 6.269 43829 Z= 0.324 Chirality : 0.047 0.175 4938 Planarity : 0.004 0.053 5745 Dihedral : 4.839 23.180 4415 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.82 % Favored : 91.89 % Rotamer: Outliers : 0.66 % Allowed : 5.94 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.12), residues: 4092 helix: 0.88 (0.18), residues: 876 sheet: -0.47 (0.16), residues: 1082 loop : -2.31 (0.12), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 112 HIS 0.004 0.001 HIS G 134 PHE 0.013 0.001 PHE H 90 TYR 0.026 0.001 TYR K 279 ARG 0.006 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 285 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6436 (mm) cc_final: 0.6111 (tp) REVERT: C 113 GLU cc_start: 0.5516 (mm-30) cc_final: 0.5237 (mm-30) REVERT: E 164 GLU cc_start: 0.3911 (mm-30) cc_final: 0.3620 (mm-30) REVERT: E 307 MET cc_start: 0.7973 (tpt) cc_final: 0.6357 (mpp) REVERT: F 94 MET cc_start: 0.8383 (tpt) cc_final: 0.7998 (tpt) REVERT: F 321 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7118 (mt-10) REVERT: H 279 TYR cc_start: 0.8238 (m-80) cc_final: 0.6783 (t80) REVERT: H 382 ILE cc_start: 0.6623 (mt) cc_final: 0.6420 (mt) REVERT: G 279 TYR cc_start: 0.8505 (m-80) cc_final: 0.8195 (m-10) REVERT: J 279 TYR cc_start: 0.8169 (m-80) cc_final: 0.7962 (m-80) REVERT: K 279 TYR cc_start: 0.8477 (m-80) cc_final: 0.7588 (m-10) REVERT: K 382 ILE cc_start: 0.6449 (mt) cc_final: 0.6248 (mt) outliers start: 22 outliers final: 13 residues processed: 295 average time/residue: 0.4221 time to fit residues: 205.4735 Evaluate side-chains 291 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain G residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 249 optimal weight: 0.0470 chunk 101 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 ASN E 181 GLN g 199 ASN h 38 ASN h 208 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32179 Z= 0.276 Angle : 0.582 7.750 43829 Z= 0.317 Chirality : 0.046 0.238 4938 Planarity : 0.004 0.052 5745 Dihedral : 5.001 23.367 4415 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.26 % Favored : 91.50 % Rotamer: Outliers : 1.11 % Allowed : 8.58 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4092 helix: 1.07 (0.18), residues: 858 sheet: -0.59 (0.16), residues: 1092 loop : -2.37 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.004 0.001 HIS g 90 PHE 0.014 0.001 PHE F 190 TYR 0.024 0.001 TYR G 279 ARG 0.006 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 279 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8932 (tttm) cc_final: 0.8603 (ttmm) REVERT: C 121 ILE cc_start: 0.8259 (pt) cc_final: 0.7942 (tt) REVERT: E 164 GLU cc_start: 0.3882 (mm-30) cc_final: 0.3658 (mm-30) REVERT: E 351 GLU cc_start: 0.4940 (mt-10) cc_final: 0.4236 (mt-10) REVERT: F 112 TRP cc_start: 0.8059 (OUTLIER) cc_final: 0.7398 (t60) REVERT: F 321 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7096 (mt-10) REVERT: H 279 TYR cc_start: 0.8222 (m-80) cc_final: 0.6285 (t80) REVERT: H 307 MET cc_start: 0.8180 (tpp) cc_final: 0.7937 (tpp) REVERT: K 279 TYR cc_start: 0.8530 (m-80) cc_final: 0.7943 (m-80) REVERT: K 310 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8417 (mm-40) outliers start: 37 outliers final: 22 residues processed: 302 average time/residue: 0.3937 time to fit residues: 197.0726 Evaluate side-chains 290 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 267 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain K residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 chunk 390 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 349 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 GLN E 181 GLN g 199 ASN h 38 ASN G 119 GLN I 143 ASN K 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32179 Z= 0.294 Angle : 0.590 7.923 43829 Z= 0.322 Chirality : 0.047 0.264 4938 Planarity : 0.004 0.048 5745 Dihedral : 5.114 23.845 4415 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.80 % Favored : 90.98 % Rotamer: Outliers : 1.59 % Allowed : 10.37 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4092 helix: 1.09 (0.18), residues: 858 sheet: -0.67 (0.16), residues: 1086 loop : -2.42 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.004 0.001 HIS G 134 PHE 0.014 0.001 PHE F 190 TYR 0.022 0.001 TYR K 279 ARG 0.006 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 275 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7940 (m-30) cc_final: 0.7659 (m-30) REVERT: A 352 LYS cc_start: 0.8949 (tttm) cc_final: 0.8613 (ttmm) REVERT: C 113 GLU cc_start: 0.5534 (mm-30) cc_final: 0.5285 (mm-30) REVERT: C 121 ILE cc_start: 0.8188 (pt) cc_final: 0.7894 (tt) REVERT: D 113 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: E 164 GLU cc_start: 0.3595 (mm-30) cc_final: 0.3330 (mm-30) REVERT: E 351 GLU cc_start: 0.4673 (mt-10) cc_final: 0.4038 (mt-10) REVERT: F 112 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7629 (t60) REVERT: F 307 MET cc_start: 0.8108 (mmm) cc_final: 0.7894 (tpt) REVERT: F 321 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7127 (mt-10) REVERT: g 108 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7682 (t80) REVERT: h 108 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8660 (m-10) REVERT: H 307 MET cc_start: 0.8147 (tpp) cc_final: 0.7894 (tpp) outliers start: 53 outliers final: 33 residues processed: 310 average time/residue: 0.3950 time to fit residues: 202.4296 Evaluate side-chains 307 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 270 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain f residue 206 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 290 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN h 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32179 Z= 0.163 Angle : 0.523 9.091 43829 Z= 0.282 Chirality : 0.044 0.158 4938 Planarity : 0.004 0.043 5745 Dihedral : 4.720 23.570 4415 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.62 % Favored : 92.18 % Rotamer: Outliers : 1.62 % Allowed : 11.27 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4092 helix: 1.26 (0.18), residues: 862 sheet: -0.63 (0.16), residues: 1069 loop : -2.36 (0.11), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.002 0.001 HIS I 134 PHE 0.008 0.001 PHE J 90 TYR 0.018 0.001 TYR J 357 ARG 0.003 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 283 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7902 (m-30) cc_final: 0.7630 (m-30) REVERT: C 121 ILE cc_start: 0.8080 (pt) cc_final: 0.7811 (tt) REVERT: E 164 GLU cc_start: 0.3987 (mm-30) cc_final: 0.3773 (mm-30) REVERT: E 351 GLU cc_start: 0.4712 (mt-10) cc_final: 0.4006 (mt-10) REVERT: F 112 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7412 (t60) REVERT: F 307 MET cc_start: 0.8138 (mmm) cc_final: 0.7826 (tpt) REVERT: g 108 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7680 (t80) REVERT: h 108 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8693 (m-10) REVERT: H 307 MET cc_start: 0.8100 (tpp) cc_final: 0.7897 (tpp) REVERT: H 311 GLU cc_start: 0.7575 (pm20) cc_final: 0.7369 (pm20) REVERT: I 382 ILE cc_start: 0.6540 (mt) cc_final: 0.6220 (mt) outliers start: 54 outliers final: 33 residues processed: 321 average time/residue: 0.3902 time to fit residues: 206.5076 Evaluate side-chains 308 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 272 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain f residue 206 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 229 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 32 optimal weight: 0.0040 chunk 129 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN g 199 ASN h 38 ASN ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32179 Z= 0.168 Angle : 0.524 9.623 43829 Z= 0.282 Chirality : 0.044 0.191 4938 Planarity : 0.003 0.047 5745 Dihedral : 4.602 22.345 4415 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.99 % Favored : 91.84 % Rotamer: Outliers : 1.59 % Allowed : 11.78 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4092 helix: 1.30 (0.19), residues: 864 sheet: -0.64 (0.16), residues: 1069 loop : -2.34 (0.11), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.002 0.001 HIS G 134 PHE 0.009 0.001 PHE F 190 TYR 0.018 0.001 TYR J 279 ARG 0.004 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 285 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7921 (m-30) cc_final: 0.7627 (m-30) REVERT: B 382 ILE cc_start: 0.6991 (tp) cc_final: 0.6782 (mm) REVERT: C 318 LEU cc_start: 0.8843 (tp) cc_final: 0.8592 (tp) REVERT: E 164 GLU cc_start: 0.3583 (mm-30) cc_final: 0.3346 (mm-30) REVERT: E 351 GLU cc_start: 0.4693 (mt-10) cc_final: 0.3964 (mt-10) REVERT: F 94 MET cc_start: 0.8429 (tpt) cc_final: 0.7915 (tpt) REVERT: F 112 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.7426 (t60) REVERT: F 307 MET cc_start: 0.8121 (mmm) cc_final: 0.7766 (tpt) REVERT: g 108 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7756 (t80) REVERT: h 108 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: H 310 GLN cc_start: 0.8385 (mm110) cc_final: 0.8115 (mm-40) REVERT: H 382 ILE cc_start: 0.6832 (mt) cc_final: 0.6587 (mt) REVERT: I 382 ILE cc_start: 0.6513 (mt) cc_final: 0.6193 (mt) outliers start: 53 outliers final: 39 residues processed: 322 average time/residue: 0.4016 time to fit residues: 215.7425 Evaluate side-chains 322 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain f residue 206 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 218 optimal weight: 0.3980 chunk 389 optimal weight: 0.3980 chunk 243 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 199 ASN h 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32179 Z= 0.166 Angle : 0.522 11.085 43829 Z= 0.280 Chirality : 0.044 0.180 4938 Planarity : 0.003 0.042 5745 Dihedral : 4.526 22.942 4415 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 1.62 % Allowed : 12.11 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 4092 helix: 1.31 (0.19), residues: 859 sheet: -0.62 (0.16), residues: 1069 loop : -2.31 (0.11), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 112 HIS 0.002 0.001 HIS G 134 PHE 0.008 0.001 PHE H 90 TYR 0.021 0.001 TYR K 279 ARG 0.008 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7907 (m-30) cc_final: 0.7615 (m-30) REVERT: B 382 ILE cc_start: 0.7154 (tp) cc_final: 0.6951 (mm) REVERT: A 311 GLU cc_start: 0.8276 (mp0) cc_final: 0.7811 (mp0) REVERT: C 123 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6265 (mt-10) REVERT: C 318 LEU cc_start: 0.8848 (tp) cc_final: 0.8613 (tp) REVERT: E 164 GLU cc_start: 0.3709 (mm-30) cc_final: 0.3407 (mm-30) REVERT: E 351 GLU cc_start: 0.4652 (mt-10) cc_final: 0.3940 (mt-10) REVERT: F 112 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7434 (t60) REVERT: g 108 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.7738 (t80) REVERT: h 108 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8702 (m-10) REVERT: H 307 MET cc_start: 0.7850 (tpp) cc_final: 0.7506 (tpt) REVERT: H 382 ILE cc_start: 0.6711 (mt) cc_final: 0.6502 (mt) REVERT: I 382 ILE cc_start: 0.6399 (mt) cc_final: 0.6109 (mt) REVERT: J 95 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8123 (p) outliers start: 54 outliers final: 36 residues processed: 318 average time/residue: 0.3875 time to fit residues: 204.8169 Evaluate side-chains 315 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 206 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 306 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 GLN A 119 GLN g 199 ASN h 38 ASN H 310 GLN I 192 ASN K 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 32179 Z= 0.303 Angle : 0.596 11.747 43829 Z= 0.324 Chirality : 0.047 0.246 4938 Planarity : 0.004 0.046 5745 Dihedral : 5.008 23.716 4415 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.94 % Favored : 90.86 % Rotamer: Outliers : 1.59 % Allowed : 12.17 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4092 helix: 1.19 (0.19), residues: 858 sheet: -0.72 (0.16), residues: 1091 loop : -2.40 (0.11), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 112 HIS 0.004 0.001 HIS G 134 PHE 0.014 0.001 PHE F 190 TYR 0.027 0.002 TYR K 279 ARG 0.004 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 269 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7919 (m-30) cc_final: 0.7637 (m-30) REVERT: B 382 ILE cc_start: 0.7311 (tp) cc_final: 0.7101 (mm) REVERT: C 121 ILE cc_start: 0.8133 (pt) cc_final: 0.7819 (tt) REVERT: D 113 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: E 164 GLU cc_start: 0.3556 (mm-30) cc_final: 0.3129 (mm-30) REVERT: E 351 GLU cc_start: 0.4736 (mt-10) cc_final: 0.3957 (mt-10) REVERT: F 112 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7333 (t60) REVERT: g 108 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.7954 (t80) REVERT: h 108 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8707 (m-10) REVERT: H 113 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: H 382 ILE cc_start: 0.6807 (mt) cc_final: 0.6559 (mt) REVERT: I 279 TYR cc_start: 0.8384 (m-80) cc_final: 0.8180 (m-80) REVERT: I 382 ILE cc_start: 0.6426 (mt) cc_final: 0.6173 (mt) REVERT: J 95 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8363 (p) outliers start: 53 outliers final: 37 residues processed: 307 average time/residue: 0.3912 time to fit residues: 199.9273 Evaluate side-chains 310 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain H residue 112 TRP Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 9.9990 chunk 373 optimal weight: 10.9990 chunk 340 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 343 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 38 ASN H 310 GLN J 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32179 Z= 0.311 Angle : 0.600 12.458 43829 Z= 0.326 Chirality : 0.047 0.220 4938 Planarity : 0.004 0.044 5745 Dihedral : 5.132 24.494 4415 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.70 % Favored : 91.08 % Rotamer: Outliers : 1.74 % Allowed : 12.17 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4092 helix: 1.11 (0.18), residues: 859 sheet: -0.71 (0.16), residues: 1065 loop : -2.43 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.004 0.001 HIS g 90 PHE 0.013 0.001 PHE H 90 TYR 0.022 0.001 TYR K 279 ARG 0.004 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7925 (m-30) cc_final: 0.7634 (m-30) REVERT: B 382 ILE cc_start: 0.7389 (tp) cc_final: 0.7127 (mm) REVERT: A 311 GLU cc_start: 0.8365 (mp0) cc_final: 0.7917 (mp0) REVERT: C 121 ILE cc_start: 0.8145 (pt) cc_final: 0.7867 (tt) REVERT: D 113 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: E 164 GLU cc_start: 0.3614 (mm-30) cc_final: 0.3211 (mm-30) REVERT: E 351 GLU cc_start: 0.5262 (mt-10) cc_final: 0.4545 (mt-10) REVERT: F 112 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.7421 (t60) REVERT: g 108 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8074 (t80) REVERT: h 108 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8728 (m-10) REVERT: H 113 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: H 382 ILE cc_start: 0.6829 (mt) cc_final: 0.6561 (mt) REVERT: I 382 ILE cc_start: 0.6528 (mt) cc_final: 0.6247 (mt) REVERT: J 95 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (p) outliers start: 58 outliers final: 41 residues processed: 309 average time/residue: 0.3940 time to fit residues: 201.6065 Evaluate side-chains 311 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 0.2980 chunk 238 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 402 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32179 Z= 0.297 Angle : 0.599 12.818 43829 Z= 0.325 Chirality : 0.047 0.217 4938 Planarity : 0.004 0.044 5745 Dihedral : 5.136 24.996 4415 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.90 % Favored : 90.88 % Rotamer: Outliers : 1.53 % Allowed : 12.29 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.12), residues: 4092 helix: 1.10 (0.18), residues: 859 sheet: -0.77 (0.15), residues: 1088 loop : -2.47 (0.11), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.004 0.001 HIS G 134 PHE 0.013 0.001 PHE H 90 TYR 0.025 0.001 TYR G 279 ARG 0.004 0.000 ARG I 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7900 (m-30) cc_final: 0.7608 (m-30) REVERT: B 382 ILE cc_start: 0.7504 (tp) cc_final: 0.7214 (mm) REVERT: C 121 ILE cc_start: 0.8160 (pt) cc_final: 0.7866 (tt) REVERT: D 113 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: E 164 GLU cc_start: 0.3631 (mm-30) cc_final: 0.3273 (mm-30) REVERT: E 307 MET cc_start: 0.7776 (tpt) cc_final: 0.6509 (mtt) REVERT: E 351 GLU cc_start: 0.5351 (mt-10) cc_final: 0.4645 (mt-10) REVERT: F 112 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.7389 (t60) REVERT: g 108 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8065 (t80) REVERT: g 115 GLU cc_start: 0.7651 (pm20) cc_final: 0.7317 (pm20) REVERT: h 108 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8694 (m-10) REVERT: H 113 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: H 382 ILE cc_start: 0.6804 (mt) cc_final: 0.6544 (mt) REVERT: I 382 ILE cc_start: 0.6533 (mt) cc_final: 0.6266 (mt) REVERT: J 95 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8330 (p) outliers start: 51 outliers final: 43 residues processed: 296 average time/residue: 0.4009 time to fit residues: 197.7611 Evaluate side-chains 313 residues out of total 3335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 120 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 156 ASP Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 112 TRP Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 295 optimal weight: 0.0270 chunk 47 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.062044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.052957 restraints weight = 78663.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.054581 restraints weight = 43314.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.055680 restraints weight = 27985.374| |-----------------------------------------------------------------------------| r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32179 Z= 0.145 Angle : 0.522 12.381 43829 Z= 0.278 Chirality : 0.044 0.181 4938 Planarity : 0.003 0.044 5745 Dihedral : 4.540 23.961 4415 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.55 % Favored : 92.18 % Rotamer: Outliers : 1.20 % Allowed : 12.77 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 4092 helix: 1.30 (0.19), residues: 859 sheet: -0.75 (0.16), residues: 1101 loop : -2.34 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 232 HIS 0.001 0.000 HIS J 134 PHE 0.008 0.001 PHE C 319 TYR 0.020 0.001 TYR J 357 ARG 0.004 0.000 ARG B 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5722.00 seconds wall clock time: 108 minutes 2.23 seconds (6482.23 seconds total)