Starting phenix.real_space_refine on Sun Jul 21 01:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/07_2024/8vuw_43542_neut.cif" } resolution = 3.19 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= 0.002 sd= 0.026 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 P 5 5.49 5 S 30 5.16 5 C 8545 2.51 5 N 2130 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13055 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "B" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "C" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "D" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "E" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 106 Unusual residues: {'DHL': 1, 'PGW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLN A 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN A 233 " occ=0.40 residue: pdb=" N AGLN B 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN B 233 " occ=0.40 residue: pdb=" N AGLN C 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN C 233 " occ=0.40 residue: pdb=" N AGLN D 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN D 233 " occ=0.40 residue: pdb=" N AGLN E 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN E 233 " occ=0.40 Time building chain proxies: 12.48, per 1000 atoms: 0.96 Number of scatterers: 13055 At special positions: 0 Unit cell: (89.723, 91.885, 123.234, 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) S 30 16.00 P 5 15.00 O 2345 8.00 N 2130 7.00 C 8545 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: 4.79 Conformation dependent library (CDL) restraints added in 4.5 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 37.8% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.731A pdb=" N LEU B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.731A pdb=" N LEU C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU E 232 " --> pdb=" O PHE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 302 through 321 removed outlier: 3.912A pdb=" N LEU E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER A 84 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 107 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 86 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 105 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY A 88 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN A 103 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS A 90 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ILE A 101 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU A 92 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG A 99 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.209A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER B 84 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 107 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 86 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 105 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY B 88 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ASN B 103 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS B 90 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE B 101 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 92 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG B 99 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.209A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SER C 84 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU C 107 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP C 86 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 105 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY C 88 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN C 103 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS C 90 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE C 101 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU C 92 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG C 99 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER D 84 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU D 107 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP D 86 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG D 105 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY D 88 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN D 103 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LYS D 90 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ILE D 101 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU D 92 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG D 99 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.622A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.622A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER E 84 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU E 107 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP E 86 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG E 105 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLY E 88 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN E 103 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LYS E 90 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE E 101 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU E 92 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N ARG E 99 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1800 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: 4.00 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2045 1.31 - 1.43: 3925 1.43 - 1.56: 7370 1.56 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 13400 Sorted by residual: bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 PGW B 401 " pdb=" O01 PGW B 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 403 " pdb=" O01 PGW A 403 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.46: 392 106.46 - 113.40: 7185 113.40 - 120.34: 5006 120.34 - 127.29: 5433 127.29 - 134.23: 169 Bond angle restraints: 18185 Sorted by residual: angle pdb=" N THR B 234 " pdb=" CA THR B 234 " pdb=" C THR B 234 " ideal model delta sigma weight residual 111.07 106.93 4.14 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR C 234 " pdb=" CA THR C 234 " pdb=" C THR C 234 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR E 234 " pdb=" CA THR E 234 " pdb=" C THR E 234 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR A 234 " pdb=" CA THR A 234 " pdb=" C THR A 234 " ideal model delta sigma weight residual 111.07 106.95 4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N THR D 234 " pdb=" CA THR D 234 " pdb=" C THR D 234 " ideal model delta sigma weight residual 111.07 106.97 4.10 1.07e+00 8.73e-01 1.46e+01 ... (remaining 18180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.37: 7505 27.37 - 54.75: 300 54.75 - 82.12: 65 82.12 - 109.49: 10 109.49 - 136.86: 15 Dihedral angle restraints: 7895 sinusoidal: 3315 harmonic: 4580 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.21 -136.86 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C03 PGW D 401 " pdb=" C01 PGW D 401 " pdb=" C02 PGW D 401 " pdb=" O03 PGW D 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.20 -136.85 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.19 -136.84 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 7892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1269 0.046 - 0.092: 486 0.092 - 0.138: 187 0.138 - 0.183: 23 0.183 - 0.229: 15 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CB VAL D 222 " pdb=" CA VAL D 222 " pdb=" CG1 VAL D 222 " pdb=" CG2 VAL D 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL C 222 " pdb=" CA VAL C 222 " pdb=" CG1 VAL C 222 " pdb=" CG2 VAL C 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 222 " pdb=" CA VAL B 222 " pdb=" CG1 VAL B 222 " pdb=" CG2 VAL B 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1977 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 50 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO C 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO D 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 50 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO E 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " -0.021 5.00e-02 4.00e+02 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3539 2.80 - 3.33: 11312 3.33 - 3.85: 22408 3.85 - 4.38: 26884 4.38 - 4.90: 46014 Nonbonded interactions: 110157 Sorted by model distance: nonbonded pdb=" ND2 ASN B 68 " pdb=" NE2 GLN C 62 " model vdw 2.280 3.200 nonbonded pdb=" OD1 ASN C 154 " pdb=" NH1 ARG C 163 " model vdw 2.284 2.520 nonbonded pdb=" OD1 ASN E 154 " pdb=" NH1 ARG E 163 " model vdw 2.285 2.520 nonbonded pdb=" ND2 ASN C 68 " pdb=" NE2 GLN D 62 " model vdw 2.285 3.200 nonbonded pdb=" OD1 ASN B 154 " pdb=" NH1 ARG B 163 " model vdw 2.285 2.520 ... (remaining 110152 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 11 through 232 or resid 234 through 321)) selection = (chain 'B' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'C' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'D' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'E' and (resid 11 through 232 or resid 234 through 321)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 45.340 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.007 0.085 13400 Z= 0.432 Angle : 0.979 10.917 18185 Z= 0.464 Chirality : 0.056 0.229 1980 Planarity : 0.005 0.038 2300 Dihedral : 17.622 136.865 4945 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % 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: -1.89 (0.20), residues: 1560 helix: -1.44 (0.18), residues: 570 sheet: 0.07 (0.23), residues: 465 loop : -2.08 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 161 HIS 0.004 0.002 HIS C 177 PHE 0.017 0.003 PHE D 223 TYR 0.015 0.002 TYR E 245 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.444 Fit side-chains REVERT: A 161 TRP cc_start: 0.8276 (m-10) cc_final: 0.7986 (m-90) REVERT: A 208 PHE cc_start: 0.8572 (t80) cc_final: 0.8349 (t80) REVERT: B 251 ASN cc_start: 0.8334 (m110) cc_final: 0.8068 (m110) REVERT: C 173 ILE cc_start: 0.8963 (mm) cc_final: 0.8733 (mm) REVERT: D 148 TYR cc_start: 0.8167 (m-80) cc_final: 0.7640 (m-80) REVERT: E 90 LYS cc_start: 0.8645 (pttp) cc_final: 0.8440 (pttp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2384 time to fit residues: 78.5865 Evaluate side-chains 172 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 233 GLN B B 68 ASN B 233 GLN B C 68 ASN C 233 GLN B C 251 ASN D 68 ASN D 233 GLN B E 68 ASN E 233 GLN B Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13400 Z= 0.271 Angle : 0.599 6.798 18185 Z= 0.299 Chirality : 0.046 0.144 1980 Planarity : 0.003 0.025 2300 Dihedral : 15.723 142.020 1965 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.86 % Allowed : 4.80 % Favored : 94.34 % 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: -1.18 (0.21), residues: 1560 helix: -0.16 (0.22), residues: 585 sheet: 0.05 (0.24), residues: 440 loop : -2.12 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 161 HIS 0.002 0.001 HIS C 177 PHE 0.013 0.002 PHE B 121 TYR 0.011 0.001 TYR A 204 ARG 0.003 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.711 Fit side-chains REVERT: A 224 TRP cc_start: 0.7533 (m100) cc_final: 0.7287 (m100) REVERT: A 230 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6193 (mp0) REVERT: C 173 ILE cc_start: 0.8926 (mm) cc_final: 0.8725 (mm) REVERT: D 36 ASP cc_start: 0.7597 (t70) cc_final: 0.7365 (t70) REVERT: D 148 TYR cc_start: 0.8296 (m-80) cc_final: 0.7716 (m-80) REVERT: E 68 ASN cc_start: 0.7939 (m-40) cc_final: 0.7537 (m-40) outliers start: 7 outliers final: 2 residues processed: 187 average time/residue: 0.2334 time to fit residues: 64.9813 Evaluate side-chains 162 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN B 89 ASN C 89 ASN D 89 ASN E 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13400 Z= 0.180 Angle : 0.532 8.118 18185 Z= 0.263 Chirality : 0.044 0.135 1980 Planarity : 0.003 0.022 2300 Dihedral : 14.525 139.944 1965 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.08 % Allowed : 6.24 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1560 helix: 0.28 (0.23), residues: 585 sheet: -0.05 (0.23), residues: 455 loop : -1.94 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.001 0.000 HIS B 177 PHE 0.014 0.001 PHE B 228 TYR 0.007 0.001 TYR E 148 ARG 0.003 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.492 Fit side-chains REVERT: A 224 TRP cc_start: 0.7456 (m100) cc_final: 0.7237 (m100) REVERT: B 251 ASN cc_start: 0.8326 (m110) cc_final: 0.8032 (m110) REVERT: C 173 ILE cc_start: 0.8895 (mm) cc_final: 0.8672 (mm) REVERT: D 148 TYR cc_start: 0.8189 (m-80) cc_final: 0.7737 (m-80) REVERT: E 68 ASN cc_start: 0.7843 (m-40) cc_final: 0.7253 (m-40) REVERT: E 114 MET cc_start: 0.8759 (mtt) cc_final: 0.8216 (mtt) outliers start: 10 outliers final: 6 residues processed: 166 average time/residue: 0.2458 time to fit residues: 60.1803 Evaluate side-chains 166 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 60 ASN C 264 GLN D 251 ASN E 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13400 Z= 0.360 Angle : 0.617 7.066 18185 Z= 0.312 Chirality : 0.047 0.156 1980 Planarity : 0.003 0.028 2300 Dihedral : 14.732 141.416 1965 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.22 % Allowed : 7.67 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1560 helix: 0.62 (0.24), residues: 555 sheet: 0.01 (0.25), residues: 435 loop : -1.97 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.028 0.002 PHE A 228 TYR 0.016 0.002 TYR A 204 ARG 0.004 0.000 ARG D 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.359 Fit side-chains REVERT: C 173 ILE cc_start: 0.9029 (mm) cc_final: 0.8795 (mm) REVERT: D 148 TYR cc_start: 0.8365 (m-80) cc_final: 0.7743 (m-80) REVERT: D 224 TRP cc_start: 0.7637 (m100) cc_final: 0.7399 (m100) outliers start: 12 outliers final: 10 residues processed: 162 average time/residue: 0.2504 time to fit residues: 59.7092 Evaluate side-chains 162 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13400 Z= 0.173 Angle : 0.524 7.954 18185 Z= 0.259 Chirality : 0.044 0.135 1980 Planarity : 0.003 0.020 2300 Dihedral : 14.319 138.991 1965 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.51 % Allowed : 8.17 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1560 helix: 0.46 (0.23), residues: 585 sheet: -0.06 (0.25), residues: 425 loop : -1.92 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.001 0.001 HIS C 177 PHE 0.024 0.001 PHE A 228 TYR 0.007 0.001 TYR E 148 ARG 0.003 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.350 Fit side-chains REVERT: C 97 ASP cc_start: 0.8323 (p0) cc_final: 0.8085 (p0) REVERT: C 173 ILE cc_start: 0.8928 (mm) cc_final: 0.8695 (mm) REVERT: D 148 TYR cc_start: 0.8248 (m-80) cc_final: 0.7777 (m-80) REVERT: D 224 TRP cc_start: 0.7593 (m100) cc_final: 0.7376 (m100) REVERT: E 114 MET cc_start: 0.8728 (mtt) cc_final: 0.8250 (mtt) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.2411 time to fit residues: 59.9266 Evaluate side-chains 170 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13400 Z= 0.203 Angle : 0.530 7.052 18185 Z= 0.265 Chirality : 0.044 0.135 1980 Planarity : 0.003 0.025 2300 Dihedral : 14.200 137.784 1965 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.29 % Allowed : 9.03 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1560 helix: 0.55 (0.23), residues: 585 sheet: -0.03 (0.25), residues: 425 loop : -1.86 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.026 0.001 PHE E 228 TYR 0.008 0.001 TYR A 204 ARG 0.002 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.304 Fit side-chains REVERT: B 30 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: C 97 ASP cc_start: 0.8350 (p0) cc_final: 0.8090 (p0) REVERT: C 173 ILE cc_start: 0.8941 (mm) cc_final: 0.8715 (mm) REVERT: D 148 TYR cc_start: 0.8304 (m-80) cc_final: 0.7840 (m-80) REVERT: D 224 TRP cc_start: 0.7608 (m100) cc_final: 0.7279 (m100) REVERT: E 114 MET cc_start: 0.8725 (mtt) cc_final: 0.8229 (mtt) outliers start: 13 outliers final: 10 residues processed: 163 average time/residue: 0.2459 time to fit residues: 58.9419 Evaluate side-chains 168 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13400 Z= 0.244 Angle : 0.548 6.916 18185 Z= 0.275 Chirality : 0.045 0.140 1980 Planarity : 0.003 0.026 2300 Dihedral : 14.210 137.519 1965 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.43 % Allowed : 9.10 % Favored : 89.46 % 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: -0.72 (0.22), residues: 1560 helix: 0.54 (0.23), residues: 585 sheet: -0.08 (0.25), residues: 425 loop : -1.86 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.027 0.002 PHE E 228 TYR 0.010 0.001 TYR E 204 ARG 0.002 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.388 Fit side-chains REVERT: B 30 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: C 97 ASP cc_start: 0.8374 (p0) cc_final: 0.8126 (p0) REVERT: C 173 ILE cc_start: 0.8968 (mm) cc_final: 0.8739 (mm) REVERT: D 148 TYR cc_start: 0.8312 (m-80) cc_final: 0.7811 (m-80) REVERT: D 224 TRP cc_start: 0.7626 (m100) cc_final: 0.7309 (m100) REVERT: E 114 MET cc_start: 0.8707 (mtt) cc_final: 0.8196 (mtt) outliers start: 15 outliers final: 12 residues processed: 159 average time/residue: 0.2423 time to fit residues: 56.8232 Evaluate side-chains 164 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.0020 overall best weight: 0.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13400 Z= 0.162 Angle : 0.507 7.108 18185 Z= 0.252 Chirality : 0.044 0.128 1980 Planarity : 0.003 0.025 2300 Dihedral : 13.775 135.413 1965 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.43 % Allowed : 9.25 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1560 helix: 0.65 (0.23), residues: 585 sheet: 0.00 (0.25), residues: 425 loop : -1.81 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.002 0.001 HIS B 284 PHE 0.023 0.001 PHE E 228 TYR 0.007 0.001 TYR C 203 ARG 0.003 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.371 Fit side-chains REVERT: A 54 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7358 (mtpt) REVERT: B 30 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: C 97 ASP cc_start: 0.8319 (p0) cc_final: 0.8088 (p0) REVERT: C 155 GLU cc_start: 0.7489 (tt0) cc_final: 0.7132 (mt-10) REVERT: C 173 ILE cc_start: 0.8886 (mm) cc_final: 0.8653 (mm) REVERT: D 148 TYR cc_start: 0.8167 (m-80) cc_final: 0.7755 (m-80) REVERT: D 224 TRP cc_start: 0.7617 (m100) cc_final: 0.7302 (m100) REVERT: E 114 MET cc_start: 0.8749 (mtt) cc_final: 0.8242 (mtt) outliers start: 15 outliers final: 11 residues processed: 156 average time/residue: 0.2453 time to fit residues: 56.3114 Evaluate side-chains 165 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.152 Angle : 0.500 7.024 18185 Z= 0.249 Chirality : 0.043 0.127 1980 Planarity : 0.003 0.026 2300 Dihedral : 13.442 133.034 1965 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.22 % Allowed : 9.61 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1560 helix: 0.71 (0.23), residues: 585 sheet: 0.08 (0.25), residues: 425 loop : -1.77 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 206 HIS 0.001 0.001 HIS B 285 PHE 0.024 0.001 PHE E 228 TYR 0.008 0.001 TYR C 203 ARG 0.004 0.000 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.719 Fit side-chains REVERT: A 54 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7333 (mtpt) REVERT: B 30 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: C 97 ASP cc_start: 0.8369 (p0) cc_final: 0.8113 (p0) REVERT: C 155 GLU cc_start: 0.7499 (tt0) cc_final: 0.7097 (mt-10) REVERT: C 173 ILE cc_start: 0.8863 (mm) cc_final: 0.8646 (mm) REVERT: D 125 GLN cc_start: 0.8428 (pt0) cc_final: 0.8150 (pt0) REVERT: D 148 TYR cc_start: 0.8115 (m-80) cc_final: 0.7752 (m-80) REVERT: E 114 MET cc_start: 0.8740 (mtt) cc_final: 0.8249 (mtt) outliers start: 12 outliers final: 11 residues processed: 158 average time/residue: 0.2458 time to fit residues: 57.4522 Evaluate side-chains 161 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 97 optimal weight: 4.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.209 Angle : 0.524 6.898 18185 Z= 0.263 Chirality : 0.044 0.134 1980 Planarity : 0.003 0.026 2300 Dihedral : 13.513 132.559 1965 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.15 % Allowed : 9.89 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1560 helix: 0.72 (0.23), residues: 585 sheet: 0.07 (0.25), residues: 425 loop : -1.80 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 161 HIS 0.002 0.001 HIS B 284 PHE 0.027 0.001 PHE E 228 TYR 0.009 0.001 TYR A 204 ARG 0.004 0.000 ARG C 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.454 Fit side-chains REVERT: A 54 LYS cc_start: 0.7651 (mmtm) cc_final: 0.7359 (mtpt) REVERT: B 30 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: C 97 ASP cc_start: 0.8345 (p0) cc_final: 0.8111 (p0) REVERT: C 155 GLU cc_start: 0.7563 (tt0) cc_final: 0.7109 (mt-10) REVERT: C 173 ILE cc_start: 0.8931 (mm) cc_final: 0.8699 (mm) REVERT: D 148 TYR cc_start: 0.8208 (m-80) cc_final: 0.7817 (m-80) REVERT: E 114 MET cc_start: 0.8743 (mtt) cc_final: 0.8248 (mtt) outliers start: 11 outliers final: 9 residues processed: 152 average time/residue: 0.2542 time to fit residues: 56.7841 Evaluate side-chains 161 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.149698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.113287 restraints weight = 49980.082| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.91 r_work: 0.2885 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13400 Z= 0.194 Angle : 0.518 6.603 18185 Z= 0.260 Chirality : 0.044 0.133 1980 Planarity : 0.003 0.034 2300 Dihedral : 13.386 131.861 1965 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.15 % Allowed : 9.96 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1560 helix: 0.72 (0.23), residues: 585 sheet: 0.06 (0.25), residues: 425 loop : -1.79 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.002 0.001 HIS B 284 PHE 0.026 0.001 PHE E 228 TYR 0.008 0.001 TYR A 204 ARG 0.006 0.000 ARG E 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.56 seconds wall clock time: 47 minutes 25.03 seconds (2845.03 seconds total)