Starting phenix.real_space_refine on Fri Feb 16 23:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u6d_20663/02_2024/6u6d_20663.pdb" } resolution = 3.6 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= 0.004 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 C 10564 2.51 5 N 2896 2.21 5 O 3240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ASP 226": "OD1" <-> "OD2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G ASP 309": "OD1" <-> "OD2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F ASP 300": "OD1" <-> "OD2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 254": "OD1" <-> "OD2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H ASP 300": "OD1" <-> "OD2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.90, per 1000 atoms: 0.65 Number of scatterers: 16770 At special positions: 0 Unit cell: (149.319, 149.319, 116.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 68 16.00 O 3240 8.00 N 2896 7.00 C 10564 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: 6.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 48.1% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 4.022A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 69 through 105 removed outlier: 4.556A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.658A pdb=" N GLU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.509A pdb=" N GLY A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.786A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.704A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 4.022A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 69 through 105 removed outlier: 4.555A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.703A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY C 177 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 178 " --> pdb=" O VAL C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.785A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.627A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.705A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 4.023A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 69 through 105 removed outlier: 4.556A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU E 171 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY E 177 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.785A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.705A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 4.023A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 69 through 105 removed outlier: 4.555A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY G 177 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA G 178 " --> pdb=" O VAL G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.786A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.706A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.809A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.680A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.694A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.581A pdb=" N VAL B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.990A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.681A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.695A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.580A pdb=" N VAL D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.989A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.681A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 242 removed outlier: 3.694A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 242 " --> pdb=" O LEU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.580A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.990A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 removed outlier: 3.682A pdb=" N GLU H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 202 Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 242 removed outlier: 3.693A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 242 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.581A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.989A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN A 158 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE A 317 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.586A pdb=" N ASN C 158 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE C 317 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN E 158 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE E 317 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN G 158 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE G 317 " --> pdb=" O GLY G 297 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 227 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.902A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.404A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 227 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.903A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 227 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.903A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN H 227 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.902A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 7.08 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: 5756 1.34 - 1.46: 3260 1.46 - 1.58: 7880 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 17008 Sorted by residual: bond pdb=" C VAL B 267 " pdb=" O VAL B 267 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.32e-01 bond pdb=" CA SER G 240 " pdb=" CB SER G 240 " ideal model delta sigma weight residual 1.532 1.517 0.015 1.79e-02 3.12e+03 6.94e-01 bond pdb=" C VAL H 267 " pdb=" O VAL H 267 " ideal model delta sigma weight residual 1.232 1.240 -0.007 8.90e-03 1.26e+04 6.93e-01 bond pdb=" CA SER A 240 " pdb=" CB SER A 240 " ideal model delta sigma weight residual 1.532 1.518 0.014 1.79e-02 3.12e+03 6.43e-01 bond pdb=" CA SER C 240 " pdb=" CB SER C 240 " ideal model delta sigma weight residual 1.532 1.518 0.014 1.79e-02 3.12e+03 6.43e-01 ... (remaining 17003 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 368 106.95 - 113.71: 9725 113.71 - 120.47: 6760 120.47 - 127.23: 6039 127.23 - 133.98: 116 Bond angle restraints: 23008 Sorted by residual: angle pdb=" N ILE D 334 " pdb=" CA ILE D 334 " pdb=" C ILE D 334 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.42e+00 angle pdb=" N ILE F 334 " pdb=" CA ILE F 334 " pdb=" C ILE F 334 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.25e+00 angle pdb=" N ILE B 334 " pdb=" CA ILE B 334 " pdb=" C ILE B 334 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.24e+00 angle pdb=" N ILE H 334 " pdb=" CA ILE H 334 " pdb=" C ILE H 334 " ideal model delta sigma weight residual 111.91 109.38 2.53 8.90e-01 1.26e+00 8.11e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 125.38 -3.84 1.91e+00 2.74e-01 4.05e+00 ... (remaining 23003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 8990 14.14 - 28.28: 982 28.28 - 42.42: 300 42.42 - 56.55: 52 56.55 - 70.69: 12 Dihedral angle restraints: 10336 sinusoidal: 4184 harmonic: 6152 Sorted by residual: dihedral pdb=" CA GLU B 133 " pdb=" C GLU B 133 " pdb=" N LEU B 134 " pdb=" CA LEU B 134 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU D 133 " pdb=" C GLU D 133 " pdb=" N LEU D 134 " pdb=" CA LEU D 134 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU H 133 " pdb=" C GLU H 133 " pdb=" N LEU H 134 " pdb=" CA LEU H 134 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 10333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1357 0.027 - 0.054: 813 0.054 - 0.081: 281 0.081 - 0.109: 173 0.109 - 0.136: 64 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE G 321 " pdb=" N ILE G 321 " pdb=" C ILE G 321 " pdb=" CB ILE G 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE D 321 " pdb=" N ILE D 321 " pdb=" C ILE D 321 " pdb=" CB ILE D 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 2685 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 175 " 0.005 2.00e-02 2.50e+03 9.42e-03 8.87e-01 pdb=" C VAL H 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL H 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG H 176 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 175 " 0.005 2.00e-02 2.50e+03 9.31e-03 8.66e-01 pdb=" C VAL B 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL B 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG B 176 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 175 " 0.005 2.00e-02 2.50e+03 9.30e-03 8.66e-01 pdb=" C VAL D 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL D 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG D 176 " 0.005 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 4613 2.81 - 3.39: 17415 3.39 - 3.97: 29760 3.97 - 4.56: 41610 4.56 - 5.14: 65136 Nonbonded interactions: 158534 Sorted by model distance: nonbonded pdb=" O ILE F 285 " pdb=" OG1 THR F 289 " model vdw 2.227 2.440 nonbonded pdb=" O ILE B 285 " pdb=" OG1 THR B 289 " model vdw 2.227 2.440 nonbonded pdb=" O ILE H 285 " pdb=" OG1 THR H 289 " model vdw 2.227 2.440 nonbonded pdb=" O ILE D 285 " pdb=" OG1 THR D 289 " model vdw 2.227 2.440 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.230 2.440 ... (remaining 158529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 336) selection = (chain 'C' and resid 20 through 336) selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.280 Check model and map are aligned: 0.000 Set scattering table: 0.100 Process input model: 46.800 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 0.019 17008 Z= 0.159 Angle : 0.509 6.822 23008 Z= 0.313 Chirality : 0.044 0.136 2688 Planarity : 0.002 0.019 2988 Dihedral : 12.889 70.693 6384 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -4.06 (0.14), residues: 2140 helix: -2.13 (0.14), residues: 988 sheet: -2.70 (0.22), residues: 356 loop : -3.22 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 46 HIS 0.002 0.000 HIS A 286 PHE 0.004 0.001 PHE G 75 TYR 0.010 0.001 TYR G 33 ARG 0.003 0.000 ARG G 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.614 Fit side-chains REVERT: A 33 TYR cc_start: 0.8087 (t80) cc_final: 0.7849 (t80) REVERT: A 103 GLN cc_start: 0.7601 (tp40) cc_final: 0.7347 (tp-100) REVERT: A 146 GLU cc_start: 0.8125 (tp30) cc_final: 0.7897 (tp30) REVERT: A 250 MET cc_start: 0.8435 (mtp) cc_final: 0.8221 (mtp) REVERT: A 281 LEU cc_start: 0.8491 (mt) cc_final: 0.7992 (pp) REVERT: C 146 GLU cc_start: 0.8122 (tp30) cc_final: 0.7807 (tp30) REVERT: C 250 MET cc_start: 0.8431 (mtp) cc_final: 0.8204 (mtp) REVERT: C 281 LEU cc_start: 0.8516 (mt) cc_final: 0.7985 (pp) REVERT: E 96 GLU cc_start: 0.7766 (tt0) cc_final: 0.7561 (tt0) REVERT: E 146 GLU cc_start: 0.8102 (tp30) cc_final: 0.7781 (tp30) REVERT: E 250 MET cc_start: 0.8357 (mtp) cc_final: 0.8115 (mtp) REVERT: E 281 LEU cc_start: 0.8499 (mt) cc_final: 0.8014 (pp) REVERT: G 146 GLU cc_start: 0.8115 (tp30) cc_final: 0.7798 (tp30) REVERT: G 250 MET cc_start: 0.8392 (mtp) cc_final: 0.8168 (mtp) REVERT: G 281 LEU cc_start: 0.8517 (mt) cc_final: 0.8081 (pp) REVERT: B 250 MET cc_start: 0.7966 (mtt) cc_final: 0.7601 (ttm) REVERT: D 250 MET cc_start: 0.7827 (mtt) cc_final: 0.7393 (ttm) REVERT: F 250 MET cc_start: 0.7959 (mtt) cc_final: 0.7552 (ttm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3826 time to fit residues: 182.6575 Evaluate side-chains 250 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.3980 chunk 160 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 158 ASN E 158 ASN E 174 ASN G 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17008 Z= 0.162 Angle : 0.448 6.574 23008 Z= 0.236 Chirality : 0.045 0.138 2688 Planarity : 0.003 0.041 2988 Dihedral : 3.615 15.041 2380 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.20 % Allowed : 12.09 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.16), residues: 2140 helix: -0.96 (0.16), residues: 996 sheet: -2.33 (0.23), residues: 332 loop : -2.68 (0.16), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 123 HIS 0.002 0.001 HIS E 117 PHE 0.009 0.001 PHE B 251 TYR 0.016 0.001 TYR C 33 ARG 0.005 0.000 ARG G 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 264 time to evaluate : 2.147 Fit side-chains REVERT: A 146 GLU cc_start: 0.8119 (tp30) cc_final: 0.7812 (tp30) REVERT: A 281 LEU cc_start: 0.8469 (mt) cc_final: 0.8021 (pp) REVERT: C 146 GLU cc_start: 0.8099 (tp30) cc_final: 0.7743 (tp30) REVERT: C 281 LEU cc_start: 0.8491 (mt) cc_final: 0.7947 (pp) REVERT: E 96 GLU cc_start: 0.7842 (tt0) cc_final: 0.7567 (tt0) REVERT: E 146 GLU cc_start: 0.8086 (tp30) cc_final: 0.7743 (tp30) REVERT: E 281 LEU cc_start: 0.8478 (mt) cc_final: 0.8041 (pp) REVERT: G 146 GLU cc_start: 0.8091 (tp30) cc_final: 0.7757 (tp30) REVERT: G 281 LEU cc_start: 0.8482 (mt) cc_final: 0.8042 (pp) REVERT: F 151 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8493 (mttt) outliers start: 22 outliers final: 18 residues processed: 277 average time/residue: 0.3170 time to fit residues: 128.0603 Evaluate side-chains 258 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 300 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17008 Z= 0.174 Angle : 0.432 6.600 23008 Z= 0.227 Chirality : 0.045 0.154 2688 Planarity : 0.003 0.032 2988 Dihedral : 3.479 14.872 2380 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.69 % Allowed : 15.31 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2140 helix: -0.38 (0.16), residues: 1000 sheet: -1.75 (0.25), residues: 332 loop : -2.37 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 123 HIS 0.002 0.001 HIS E 117 PHE 0.006 0.001 PHE A 75 TYR 0.027 0.002 TYR E 65 ARG 0.003 0.000 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.997 Fit side-chains REVERT: A 146 GLU cc_start: 0.8124 (tp30) cc_final: 0.7810 (tp30) REVERT: A 281 LEU cc_start: 0.8474 (mt) cc_final: 0.7885 (pp) REVERT: C 133 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7341 (tt0) REVERT: C 146 GLU cc_start: 0.8108 (tp30) cc_final: 0.7765 (tp30) REVERT: C 281 LEU cc_start: 0.8490 (mt) cc_final: 0.7968 (pp) REVERT: C 326 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7297 (mm-30) REVERT: E 65 TYR cc_start: 0.8154 (m-80) cc_final: 0.7947 (m-10) REVERT: E 96 GLU cc_start: 0.7814 (tt0) cc_final: 0.7549 (tt0) REVERT: E 146 GLU cc_start: 0.8099 (tp30) cc_final: 0.7720 (tp30) REVERT: E 281 LEU cc_start: 0.8476 (mt) cc_final: 0.7906 (pp) REVERT: G 103 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7547 (tp-100) REVERT: G 146 GLU cc_start: 0.8093 (tp30) cc_final: 0.7758 (tp30) REVERT: G 281 LEU cc_start: 0.8492 (mt) cc_final: 0.8006 (pp) outliers start: 31 outliers final: 21 residues processed: 256 average time/residue: 0.3257 time to fit residues: 120.4577 Evaluate side-chains 252 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 300 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 129 optimal weight: 0.0570 chunk 193 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17008 Z= 0.147 Angle : 0.414 6.259 23008 Z= 0.218 Chirality : 0.045 0.138 2688 Planarity : 0.003 0.034 2988 Dihedral : 3.320 14.235 2380 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.80 % Allowed : 15.47 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.17), residues: 2140 helix: 0.03 (0.16), residues: 1000 sheet: -1.34 (0.26), residues: 332 loop : -2.33 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 52 HIS 0.003 0.000 HIS A 286 PHE 0.009 0.001 PHE G 75 TYR 0.018 0.002 TYR G 33 ARG 0.006 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 1.861 Fit side-chains REVERT: A 146 GLU cc_start: 0.8109 (tp30) cc_final: 0.7767 (tp30) REVERT: A 281 LEU cc_start: 0.8481 (mt) cc_final: 0.7883 (pp) REVERT: A 326 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7290 (mm-30) REVERT: C 133 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7320 (tt0) REVERT: C 146 GLU cc_start: 0.8098 (tp30) cc_final: 0.7739 (tp30) REVERT: C 281 LEU cc_start: 0.8519 (mt) cc_final: 0.7959 (pp) REVERT: C 326 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7404 (mm-30) REVERT: E 96 GLU cc_start: 0.7810 (tt0) cc_final: 0.7558 (tt0) REVERT: E 146 GLU cc_start: 0.8083 (tp30) cc_final: 0.7694 (tp30) REVERT: E 281 LEU cc_start: 0.8488 (mt) cc_final: 0.7910 (pp) REVERT: G 146 GLU cc_start: 0.8081 (tp30) cc_final: 0.7691 (tp30) REVERT: G 281 LEU cc_start: 0.8492 (mt) cc_final: 0.7906 (pp) REVERT: G 326 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7310 (mm-30) REVERT: B 132 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: F 132 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7622 (mtm-85) REVERT: H 132 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7578 (mtm-85) outliers start: 33 outliers final: 24 residues processed: 265 average time/residue: 0.3196 time to fit residues: 122.1207 Evaluate side-chains 255 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 chunk 141 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17008 Z= 0.139 Angle : 0.408 6.858 23008 Z= 0.214 Chirality : 0.044 0.139 2688 Planarity : 0.003 0.047 2988 Dihedral : 3.252 13.828 2380 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 16.67 % Favored : 81.64 % 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: -1.22 (0.17), residues: 2140 helix: 0.38 (0.17), residues: 996 sheet: -1.05 (0.27), residues: 332 loop : -2.19 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 52 HIS 0.003 0.000 HIS C 286 PHE 0.017 0.001 PHE G 75 TYR 0.017 0.001 TYR E 51 ARG 0.005 0.000 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 2.156 Fit side-chains REVERT: A 103 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7396 (tp-100) REVERT: A 146 GLU cc_start: 0.8095 (tp30) cc_final: 0.7740 (tp30) REVERT: A 281 LEU cc_start: 0.8465 (mt) cc_final: 0.7904 (pp) REVERT: C 146 GLU cc_start: 0.8087 (tp30) cc_final: 0.7723 (tp30) REVERT: C 281 LEU cc_start: 0.8524 (mt) cc_final: 0.7969 (pp) REVERT: C 326 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7397 (mm-30) REVERT: E 96 GLU cc_start: 0.7810 (tt0) cc_final: 0.7577 (tt0) REVERT: E 146 GLU cc_start: 0.8075 (tp30) cc_final: 0.7701 (tp30) REVERT: E 281 LEU cc_start: 0.8493 (mt) cc_final: 0.7935 (pp) REVERT: E 326 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7334 (mm-30) REVERT: G 146 GLU cc_start: 0.8073 (tp30) cc_final: 0.7725 (tp30) REVERT: G 281 LEU cc_start: 0.8499 (mt) cc_final: 0.7944 (pp) REVERT: G 326 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 132 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: F 132 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: H 132 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7445 (mtm-85) outliers start: 31 outliers final: 28 residues processed: 267 average time/residue: 0.3376 time to fit residues: 129.3076 Evaluate side-chains 266 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 238 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 0.0070 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17008 Z= 0.137 Angle : 0.402 6.376 23008 Z= 0.211 Chirality : 0.044 0.136 2688 Planarity : 0.003 0.021 2988 Dihedral : 3.190 13.438 2380 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 17.43 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2140 helix: 0.70 (0.17), residues: 972 sheet: -0.93 (0.27), residues: 332 loop : -2.04 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 52 HIS 0.003 0.000 HIS C 286 PHE 0.018 0.001 PHE A 75 TYR 0.018 0.001 TYR G 51 ARG 0.005 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 249 time to evaluate : 2.074 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7387 (tp-100) REVERT: A 146 GLU cc_start: 0.8080 (tp30) cc_final: 0.7739 (tp30) REVERT: A 281 LEU cc_start: 0.8425 (mt) cc_final: 0.7920 (pp) REVERT: C 146 GLU cc_start: 0.8088 (tp30) cc_final: 0.7720 (tp30) REVERT: C 281 LEU cc_start: 0.8444 (mt) cc_final: 0.7944 (pp) REVERT: E 96 GLU cc_start: 0.7805 (tt0) cc_final: 0.7598 (tt0) REVERT: E 133 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7204 (tt0) REVERT: E 146 GLU cc_start: 0.8075 (tp30) cc_final: 0.7704 (tp30) REVERT: E 281 LEU cc_start: 0.8500 (mt) cc_final: 0.7938 (pp) REVERT: G 146 GLU cc_start: 0.8069 (tp30) cc_final: 0.7721 (tp30) REVERT: G 281 LEU cc_start: 0.8438 (mt) cc_final: 0.7945 (pp) REVERT: B 132 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7511 (mtm-85) REVERT: F 132 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: H 132 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7441 (mtm-85) outliers start: 32 outliers final: 29 residues processed: 270 average time/residue: 0.3204 time to fit residues: 125.4697 Evaluate side-chains 266 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 17008 Z= 0.322 Angle : 0.487 6.654 23008 Z= 0.255 Chirality : 0.047 0.149 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.572 13.821 2380 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.18 % Allowed : 17.54 % Favored : 80.28 % 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: -1.12 (0.17), residues: 2140 helix: 0.44 (0.17), residues: 980 sheet: -1.08 (0.27), residues: 332 loop : -2.01 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 123 HIS 0.004 0.001 HIS A 117 PHE 0.020 0.001 PHE A 75 TYR 0.020 0.002 TYR G 51 ARG 0.005 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8209 (tp30) cc_final: 0.7880 (tp30) REVERT: A 281 LEU cc_start: 0.8470 (mt) cc_final: 0.7938 (pp) REVERT: C 146 GLU cc_start: 0.8207 (tp30) cc_final: 0.7985 (tp30) REVERT: C 281 LEU cc_start: 0.8502 (mt) cc_final: 0.7978 (pp) REVERT: E 96 GLU cc_start: 0.7817 (tt0) cc_final: 0.7585 (tt0) REVERT: E 133 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7353 (tt0) REVERT: E 146 GLU cc_start: 0.8201 (tp30) cc_final: 0.7992 (tp30) REVERT: E 281 LEU cc_start: 0.8482 (mt) cc_final: 0.7960 (pp) REVERT: G 146 GLU cc_start: 0.8202 (tp30) cc_final: 0.7989 (tp30) REVERT: G 281 LEU cc_start: 0.8480 (mt) cc_final: 0.7962 (pp) outliers start: 40 outliers final: 32 residues processed: 276 average time/residue: 0.3094 time to fit residues: 124.5100 Evaluate side-chains 271 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17008 Z= 0.269 Angle : 0.465 6.762 23008 Z= 0.243 Chirality : 0.046 0.142 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.543 13.550 2380 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.29 % Allowed : 18.57 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2140 helix: 0.37 (0.16), residues: 1004 sheet: -1.04 (0.27), residues: 332 loop : -1.98 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 123 HIS 0.004 0.001 HIS C 286 PHE 0.022 0.001 PHE A 75 TYR 0.023 0.002 TYR C 51 ARG 0.004 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 1.956 Fit side-chains REVERT: A 103 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7402 (tp-100) REVERT: A 146 GLU cc_start: 0.8198 (tp30) cc_final: 0.7893 (tp30) REVERT: A 281 LEU cc_start: 0.8487 (mt) cc_final: 0.7970 (pp) REVERT: C 146 GLU cc_start: 0.8200 (tp30) cc_final: 0.7874 (tp30) REVERT: C 281 LEU cc_start: 0.8499 (mt) cc_final: 0.7969 (pp) REVERT: E 96 GLU cc_start: 0.7822 (tt0) cc_final: 0.7589 (tt0) REVERT: E 281 LEU cc_start: 0.8475 (mt) cc_final: 0.7952 (pp) REVERT: G 146 GLU cc_start: 0.8196 (tp30) cc_final: 0.7992 (tp30) REVERT: G 281 LEU cc_start: 0.8476 (mt) cc_final: 0.7952 (pp) REVERT: B 132 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: F 132 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: H 132 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7636 (mtm-85) outliers start: 42 outliers final: 38 residues processed: 269 average time/residue: 0.3042 time to fit residues: 119.8812 Evaluate side-chains 270 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 180 optimal weight: 0.4980 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 103 GLN G 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17008 Z= 0.149 Angle : 0.423 10.580 23008 Z= 0.220 Chirality : 0.045 0.143 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.324 11.707 2380 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 19.50 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2140 helix: 0.68 (0.17), residues: 1000 sheet: -0.95 (0.27), residues: 332 loop : -1.87 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 52 HIS 0.003 0.001 HIS C 286 PHE 0.022 0.001 PHE A 75 TYR 0.022 0.001 TYR C 51 ARG 0.006 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8086 (tp30) cc_final: 0.7834 (tp30) REVERT: A 281 LEU cc_start: 0.8488 (mt) cc_final: 0.7954 (pp) REVERT: C 146 GLU cc_start: 0.8132 (tp30) cc_final: 0.7841 (tp30) REVERT: C 281 LEU cc_start: 0.8456 (mt) cc_final: 0.7980 (pp) REVERT: E 96 GLU cc_start: 0.7833 (tt0) cc_final: 0.7605 (tt0) REVERT: E 146 GLU cc_start: 0.8101 (tp30) cc_final: 0.7812 (tp30) REVERT: E 281 LEU cc_start: 0.8494 (mt) cc_final: 0.7973 (pp) REVERT: G 146 GLU cc_start: 0.8122 (tp30) cc_final: 0.7836 (tp30) REVERT: G 281 LEU cc_start: 0.8496 (mt) cc_final: 0.7971 (pp) outliers start: 33 outliers final: 27 residues processed: 258 average time/residue: 0.3175 time to fit residues: 120.2920 Evaluate side-chains 261 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 17008 Z= 0.396 Angle : 0.536 10.666 23008 Z= 0.276 Chirality : 0.048 0.140 2688 Planarity : 0.003 0.025 2988 Dihedral : 3.720 14.783 2380 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.80 % Allowed : 19.34 % Favored : 78.87 % 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: -1.15 (0.17), residues: 2140 helix: 0.37 (0.16), residues: 1004 sheet: -1.53 (0.29), residues: 292 loop : -1.81 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 123 HIS 0.006 0.002 HIS G 117 PHE 0.023 0.002 PHE G 75 TYR 0.024 0.002 TYR E 51 ARG 0.004 0.000 ARG C 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8471 (mt) cc_final: 0.7963 (pp) REVERT: C 264 MET cc_start: 0.8645 (ttt) cc_final: 0.8426 (ttt) REVERT: C 281 LEU cc_start: 0.8515 (mt) cc_final: 0.7995 (pp) REVERT: E 96 GLU cc_start: 0.7830 (tt0) cc_final: 0.7597 (tt0) REVERT: E 281 LEU cc_start: 0.8473 (mt) cc_final: 0.7967 (pp) REVERT: G 281 LEU cc_start: 0.8472 (mt) cc_final: 0.7964 (pp) REVERT: F 308 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7578 (ttm-80) REVERT: H 308 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7738 (tpp80) outliers start: 33 outliers final: 30 residues processed: 254 average time/residue: 0.3202 time to fit residues: 120.3735 Evaluate side-chains 257 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 46 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS E 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103645 restraints weight = 21918.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105243 restraints weight = 19925.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106323 restraints weight = 14411.767| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17008 Z= 0.121 Angle : 0.429 10.410 23008 Z= 0.221 Chirality : 0.044 0.142 2688 Planarity : 0.002 0.022 2988 Dihedral : 3.298 12.922 2380 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.53 % Allowed : 19.83 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2140 helix: 0.85 (0.17), residues: 1000 sheet: -0.89 (0.27), residues: 332 loop : -1.76 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 46 HIS 0.003 0.001 HIS C 286 PHE 0.023 0.001 PHE G 75 TYR 0.021 0.001 TYR C 51 ARG 0.005 0.000 ARG C 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.43 seconds wall clock time: 61 minutes 11.01 seconds (3671.01 seconds total)