Starting phenix.real_space_refine on Fri Mar 15 23:30:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/03_2024/8vuw_43542_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/03_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_43542/03_2024/8vuw_43542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/03_2024/8vuw_43542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/03_2024/8vuw_43542_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuw_43542/03_2024/8vuw_43542_neut_updated.pdb" } 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-5265/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: 12.14, per 1000 atoms: 0.93 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: 4.89 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 31.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 224 removed outlier: 4.312A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.746A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.618A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 252' Processing helix chain 'A' and resid 261 through 286 Processing helix chain 'A' and resid 301 through 320 Proline residue: A 305 - end of helix 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 63 through 69 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.312A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.747A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.618A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 252' Processing helix chain 'B' and resid 261 through 286 Processing helix chain 'B' and resid 301 through 320 Proline residue: B 305 - end of helix 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 63 through 69 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.312A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.746A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.618A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 261 through 286 Processing helix chain 'C' and resid 301 through 320 Proline residue: C 305 - end of helix 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 63 through 69 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 224 removed outlier: 4.312A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.746A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.618A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 252' Processing helix chain 'D' and resid 261 through 286 Processing helix chain 'D' and resid 301 through 320 Proline residue: D 305 - end of helix 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 63 through 69 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.313A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 233 through 245 removed outlier: 3.746A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 removed outlier: 3.618A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 248 through 252' Processing helix chain 'E' and resid 261 through 286 Processing helix chain 'E' and resid 301 through 320 Proline residue: E 305 - end of helix 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= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.696A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.697A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.696A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.697A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= Q, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'E' and resid 145 through 148 removed outlier: 6.697A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'E' and resid 167 through 174 530 hydrogen bonds defined for protein. 1545 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: 3.69 Time building geometry restraints manager: 5.30 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: 3549 2.80 - 3.33: 11347 3.33 - 3.85: 22458 3.85 - 4.38: 26959 4.38 - 4.90: 46024 Nonbonded interactions: 110337 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 110332 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: 0.010 Normalize map: mean=0, sd=1: 0.240 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: 2.000 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 43.510 Find NCS groups from input model: 1.000 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- 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= 0.436 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 : 1.537 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: 0.2439 time to fit residues: 80.2583 Evaluate side-chains 172 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 68 ASN A 233 GLN B B 60 ASN B 68 ASN B 233 GLN B C 60 ASN C 68 ASN C 233 GLN B C 251 ASN D 60 ASN D 68 ASN D 233 GLN B E 60 ASN E 68 ASN E 233 GLN B Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13400 Z= 0.273 Angle : 0.586 6.939 18185 Z= 0.289 Chirality : 0.046 0.154 1980 Planarity : 0.003 0.025 2300 Dihedral : 15.524 141.766 1965 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.86 % Allowed : 4.87 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1560 helix: -0.27 (0.22), residues: 565 sheet: -0.01 (0.23), residues: 465 loop : -1.89 (0.26), residues: 530 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 D 204 ARG 0.002 0.000 ARG B 286 *********************** 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 181 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.489 Fit side-chains REVERT: A 208 PHE cc_start: 0.8512 (t80) cc_final: 0.8268 (t80) REVERT: A 224 TRP cc_start: 0.7491 (m100) cc_final: 0.7248 (m100) REVERT: A 230 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6190 (mp0) REVERT: D 36 ASP cc_start: 0.7560 (t70) cc_final: 0.7333 (t70) REVERT: D 61 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8104 (t) REVERT: D 148 TYR cc_start: 0.8313 (m-80) cc_final: 0.7731 (m-80) REVERT: E 90 LYS cc_start: 0.8728 (pttp) cc_final: 0.8484 (pttp) outliers start: 7 outliers final: 4 residues processed: 178 average time/residue: 0.2383 time to fit residues: 62.8359 Evaluate side-chains 166 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 61 THR 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: 0.8980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 0.0030 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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 B 264 GLN C 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: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.176 Angle : 0.509 6.815 18185 Z= 0.251 Chirality : 0.044 0.133 1980 Planarity : 0.003 0.022 2300 Dihedral : 14.425 138.989 1965 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.22 % Allowed : 6.02 % Favored : 92.76 % 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 (0.21), residues: 1560 helix: 0.23 (0.23), residues: 555 sheet: -0.03 (0.23), residues: 465 loop : -1.71 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 161 HIS 0.002 0.001 HIS C 177 PHE 0.011 0.001 PHE C 208 TYR 0.007 0.001 TYR A 204 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 183 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: A 224 TRP cc_start: 0.7454 (m100) cc_final: 0.7218 (m100) REVERT: D 61 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8021 (t) REVERT: D 148 TYR cc_start: 0.8201 (m-80) cc_final: 0.7742 (m-80) outliers start: 12 outliers final: 8 residues processed: 177 average time/residue: 0.2323 time to fit residues: 61.2136 Evaluate side-chains 172 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 61 THR 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: 0.9990 chunk 106 optimal weight: 0.0010 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13400 Z= 0.319 Angle : 0.579 6.891 18185 Z= 0.291 Chirality : 0.046 0.184 1980 Planarity : 0.003 0.028 2300 Dihedral : 14.562 139.823 1965 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.29 % Allowed : 7.10 % Favored : 91.61 % 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 (0.22), residues: 1560 helix: 0.34 (0.23), residues: 555 sheet: -0.14 (0.23), residues: 465 loop : -1.73 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.021 0.002 PHE E 228 TYR 0.012 0.001 TYR E 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 183 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.465 Fit side-chains REVERT: A 208 PHE cc_start: 0.8506 (t80) cc_final: 0.8288 (t80) REVERT: D 36 ASP cc_start: 0.7578 (t70) cc_final: 0.7347 (t70) REVERT: D 61 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8142 (t) REVERT: D 148 TYR cc_start: 0.8400 (m-80) cc_final: 0.7838 (m-80) REVERT: E 114 MET cc_start: 0.8691 (mtt) cc_final: 0.8236 (mtt) outliers start: 13 outliers final: 11 residues processed: 173 average time/residue: 0.2355 time to fit residues: 60.4221 Evaluate side-chains 167 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 61 THR 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: 0.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1515 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= 0.191 Angle : 0.516 6.959 18185 Z= 0.256 Chirality : 0.044 0.149 1980 Planarity : 0.003 0.023 2300 Dihedral : 14.278 137.750 1965 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.58 % Allowed : 7.74 % Favored : 90.68 % 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: -0.91 (0.21), residues: 1560 helix: 0.12 (0.22), residues: 585 sheet: -0.19 (0.23), residues: 455 loop : -1.69 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.022 0.001 PHE E 228 TYR 0.007 0.001 TYR E 148 ARG 0.002 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 181 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.504 Fit side-chains REVERT: A 208 PHE cc_start: 0.8458 (t80) cc_final: 0.8222 (t80) REVERT: D 61 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (t) REVERT: D 148 TYR cc_start: 0.8338 (m-80) cc_final: 0.7836 (m-80) REVERT: D 224 TRP cc_start: 0.7525 (m100) cc_final: 0.7211 (m100) REVERT: E 114 MET cc_start: 0.8727 (mtt) cc_final: 0.8255 (mtt) outliers start: 17 outliers final: 14 residues processed: 169 average time/residue: 0.2413 time to fit residues: 60.4159 Evaluate side-chains 175 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 B residue 61 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 61 THR 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 Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13400 Z= 0.170 Angle : 0.494 6.551 18185 Z= 0.246 Chirality : 0.044 0.155 1980 Planarity : 0.002 0.025 2300 Dihedral : 13.961 135.457 1965 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.79 % Allowed : 8.17 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1560 helix: 0.18 (0.22), residues: 585 sheet: -0.12 (0.23), residues: 455 loop : -1.63 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 161 HIS 0.002 0.001 HIS D 177 PHE 0.020 0.001 PHE E 228 TYR 0.007 0.001 TYR C 203 ARG 0.003 0.000 ARG E 163 *********************** 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 181 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 2.170 Fit side-chains REVERT: A 208 PHE cc_start: 0.8457 (t80) cc_final: 0.8227 (t80) REVERT: B 30 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: C 155 GLU cc_start: 0.7561 (tt0) cc_final: 0.7132 (mt-10) REVERT: D 148 TYR cc_start: 0.8262 (m-80) cc_final: 0.7851 (m-80) REVERT: D 224 TRP cc_start: 0.7467 (m100) cc_final: 0.7174 (m100) REVERT: E 114 MET cc_start: 0.8732 (mtt) cc_final: 0.8237 (mtt) outliers start: 20 outliers final: 15 residues processed: 169 average time/residue: 0.2346 time to fit residues: 59.1329 Evaluate side-chains 171 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 B residue 30 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 VAL 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 D residue 232 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13400 Z= 0.229 Angle : 0.524 6.866 18185 Z= 0.263 Chirality : 0.045 0.166 1980 Planarity : 0.003 0.027 2300 Dihedral : 14.003 134.944 1965 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.65 % Allowed : 8.53 % Favored : 89.82 % 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 (0.22), residues: 1560 helix: 0.20 (0.23), residues: 585 sheet: -0.12 (0.23), residues: 455 loop : -1.64 (0.28), residues: 520 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 0.025 0.001 PHE E 228 TYR 0.009 0.001 TYR A 204 ARG 0.004 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 175 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.497 Fit side-chains REVERT: A 208 PHE cc_start: 0.8525 (t80) cc_final: 0.8288 (t80) REVERT: B 30 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: D 148 TYR cc_start: 0.8337 (m-80) cc_final: 0.7857 (m-80) REVERT: D 224 TRP cc_start: 0.7541 (m100) cc_final: 0.7243 (m100) REVERT: E 114 MET cc_start: 0.8734 (mtt) cc_final: 0.8245 (mtt) outliers start: 18 outliers final: 16 residues processed: 163 average time/residue: 0.2448 time to fit residues: 59.9984 Evaluate side-chains 168 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 B residue 30 GLU Chi-restraints excluded: chain B residue 61 THR 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 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN D 60 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13400 Z= 0.305 Angle : 0.570 6.908 18185 Z= 0.287 Chirality : 0.046 0.149 1980 Planarity : 0.003 0.029 2300 Dihedral : 14.244 135.573 1965 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.72 % Allowed : 8.82 % 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: -0.88 (0.22), residues: 1560 helix: 0.15 (0.23), residues: 585 sheet: -0.18 (0.23), residues: 455 loop : -1.66 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 161 HIS 0.002 0.001 HIS A 177 PHE 0.029 0.002 PHE E 228 TYR 0.012 0.002 TYR A 204 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 172 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.587 Fit side-chains REVERT: A 208 PHE cc_start: 0.8598 (t80) cc_final: 0.8339 (t80) REVERT: B 30 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: D 36 ASP cc_start: 0.7579 (t70) cc_final: 0.7346 (t70) REVERT: D 148 TYR cc_start: 0.8399 (m-80) cc_final: 0.7820 (m-80) REVERT: D 224 TRP cc_start: 0.7629 (m100) cc_final: 0.7334 (m100) REVERT: E 68 ASN cc_start: 0.7976 (m-40) cc_final: 0.7462 (m-40) REVERT: E 114 MET cc_start: 0.8661 (mtt) cc_final: 0.8193 (mtt) outliers start: 19 outliers final: 18 residues processed: 161 average time/residue: 0.2374 time to fit residues: 56.8574 Evaluate side-chains 167 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 B residue 30 GLU Chi-restraints excluded: chain B residue 61 THR 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 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 125 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13400 Z= 0.154 Angle : 0.489 6.582 18185 Z= 0.243 Chirality : 0.043 0.136 1980 Planarity : 0.003 0.024 2300 Dihedral : 13.670 132.826 1965 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.51 % Allowed : 9.39 % Favored : 89.10 % 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: 0.20 (0.22), residues: 585 sheet: -0.09 (0.23), residues: 455 loop : -1.64 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.002 0.000 HIS C 177 PHE 0.021 0.001 PHE E 228 TYR 0.007 0.001 TYR E 203 ARG 0.004 0.000 ARG C 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 174 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.489 Fit side-chains REVERT: A 208 PHE cc_start: 0.8464 (t80) cc_final: 0.8256 (t80) REVERT: B 30 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: C 155 GLU cc_start: 0.7542 (tt0) cc_final: 0.7081 (mt-10) REVERT: D 148 TYR cc_start: 0.8198 (m-80) cc_final: 0.7723 (m-80) REVERT: D 224 TRP cc_start: 0.7507 (m100) cc_final: 0.7205 (m100) REVERT: E 114 MET cc_start: 0.8728 (mtt) cc_final: 0.8239 (mtt) outliers start: 16 outliers final: 15 residues processed: 163 average time/residue: 0.2365 time to fit residues: 58.1672 Evaluate side-chains 167 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 61 THR 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 D residue 232 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1811 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= 0.163 Angle : 0.489 6.204 18185 Z= 0.244 Chirality : 0.044 0.132 1980 Planarity : 0.003 0.028 2300 Dihedral : 13.492 131.160 1965 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.51 % Allowed : 9.46 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1560 helix: 0.18 (0.22), residues: 590 sheet: -0.02 (0.23), residues: 455 loop : -1.58 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.002 0.001 HIS A 177 PHE 0.009 0.001 PHE D 121 TYR 0.006 0.001 TYR E 203 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 169 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.554 Fit side-chains REVERT: A 54 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7363 (mtpt) REVERT: A 208 PHE cc_start: 0.8478 (t80) cc_final: 0.8269 (t80) REVERT: B 30 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6757 (tt0) REVERT: C 155 GLU cc_start: 0.7512 (tt0) cc_final: 0.7088 (mt-10) REVERT: D 148 TYR cc_start: 0.8228 (m-80) cc_final: 0.7770 (m-80) REVERT: D 224 TRP cc_start: 0.7513 (m100) cc_final: 0.7207 (m100) REVERT: E 114 MET cc_start: 0.8729 (mtt) cc_final: 0.8254 (mtt) outliers start: 16 outliers final: 13 residues processed: 158 average time/residue: 0.2328 time to fit residues: 55.3150 Evaluate side-chains 164 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 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 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.154589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.123622 restraints weight = 49584.002| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.51 r_work: 0.2880 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1834 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= 0.175 Angle : 0.492 6.926 18185 Z= 0.247 Chirality : 0.044 0.159 1980 Planarity : 0.003 0.026 2300 Dihedral : 13.353 130.320 1965 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.51 % Allowed : 9.32 % 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: -0.70 (0.22), residues: 1560 helix: 0.19 (0.22), residues: 590 sheet: 0.02 (0.24), residues: 455 loop : -1.56 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.002 0.001 HIS A 284 PHE 0.009 0.001 PHE E 121 TYR 0.007 0.001 TYR D 204 ARG 0.005 0.000 ARG C 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.68 seconds wall clock time: 48 minutes 14.30 seconds (2894.30 seconds total)