Starting phenix.real_space_refine on Sat Jul 20 14:13:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/07_2024/8twz_41673.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 7360 2.51 5 N 1850 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11270 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "C" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "D" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "E" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.21, per 1000 atoms: 0.55 Number of scatterers: 11270 At special positions: 0 Unit cell: (89.723, 89.723, 112.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 2040 8.00 N 1850 7.00 C 7360 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: 4.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 31.4% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) 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 221 Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 284 Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) 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 221 Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.683A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'C' and resid 61 through 70 removed outlier: 4.002A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) 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 221 Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 284 Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) 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 221 Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 284 Processing helix chain 'E' and resid 61 through 70 removed outlier: 4.000A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) 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 221 Processing helix chain 'E' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 284 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 59 removed outlier: 4.118A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.606A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.706A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.706A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 620 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: 3.84 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3286 1.34 - 1.45: 2013 1.45 - 1.57: 6246 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 11585 Sorted by residual: bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.83e+00 bond pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.58e+00 ... (remaining 11580 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.19: 395 107.19 - 113.95: 6342 113.95 - 120.70: 4697 120.70 - 127.46: 4205 127.46 - 134.21: 151 Bond angle restraints: 15790 Sorted by residual: angle pdb=" C VAL A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta sigma weight residual 122.64 116.80 5.84 1.77e+00 3.19e-01 1.09e+01 angle pdb=" C VAL B 58 " pdb=" N GLU B 59 " pdb=" CA GLU B 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 angle pdb=" C VAL D 58 " pdb=" N GLU D 59 " pdb=" CA GLU D 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 6041 15.96 - 31.92: 544 31.92 - 47.87: 115 47.87 - 63.83: 40 63.83 - 79.79: 15 Dihedral angle restraints: 6755 sinusoidal: 2715 harmonic: 4040 Sorted by residual: dihedral pdb=" CG ARG B 255 " pdb=" CD ARG B 255 " pdb=" NE ARG B 255 " pdb=" CZ ARG B 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.53 48.47 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG E 255 " pdb=" CD ARG E 255 " pdb=" NE ARG E 255 " pdb=" CZ ARG E 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.54 48.46 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG D 255 " pdb=" CD ARG D 255 " pdb=" NE ARG D 255 " pdb=" CZ ARG D 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.58 48.42 2 1.50e+01 4.44e-03 1.19e+01 ... (remaining 6752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1131 0.041 - 0.082: 399 0.082 - 0.124: 165 0.124 - 0.165: 34 0.165 - 0.206: 11 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CB THR D 149 " pdb=" CA THR D 149 " pdb=" OG1 THR D 149 " pdb=" CG2 THR D 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR C 149 " pdb=" CA THR C 149 " pdb=" OG1 THR C 149 " pdb=" CG2 THR C 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 149 " pdb=" CA THR A 149 " pdb=" OG1 THR A 149 " pdb=" CG2 THR A 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1737 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.53e+00 pdb=" NE ARG B 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 255 " -0.185 9.50e-02 1.11e+02 8.35e-02 5.52e+00 pdb=" NE ARG E 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.52e+00 pdb=" NE ARG A 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 255 " -0.000 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3369 2.83 - 3.35: 9583 3.35 - 3.86: 18756 3.86 - 4.38: 21893 4.38 - 4.90: 39594 Nonbonded interactions: 93195 Sorted by model distance: nonbonded pdb=" OH TYR A 245 " pdb=" OH TYR E 270 " model vdw 2.309 2.440 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.329 2.440 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.329 2.440 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.330 2.440 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.330 2.440 ... (remaining 93190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.000 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 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: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11585 Z= 0.277 Angle : 0.715 7.466 15790 Z= 0.371 Chirality : 0.052 0.206 1740 Planarity : 0.006 0.084 2005 Dihedral : 14.021 79.790 4145 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.87 (0.22), residues: 1360 helix: -0.43 (0.23), residues: 425 sheet: 0.71 (0.25), residues: 465 loop : -2.01 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 206 HIS 0.004 0.001 HIS D 177 PHE 0.009 0.002 PHE E 116 TYR 0.013 0.001 TYR B 248 ARG 0.020 0.002 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.233 Fit side-chains REVERT: B 129 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 114 MET cc_start: 0.8537 (ttm) cc_final: 0.8286 (ttm) REVERT: C 263 ASP cc_start: 0.7575 (m-30) cc_final: 0.7285 (m-30) REVERT: D 172 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2533 time to fit residues: 67.3737 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN B 60 ASN B 89 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 89 ASN D 60 ASN D 89 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 89 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11585 Z= 0.321 Angle : 0.578 7.129 15790 Z= 0.292 Chirality : 0.049 0.137 1740 Planarity : 0.004 0.027 2005 Dihedral : 4.479 16.251 1510 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.97 % Allowed : 9.76 % Favored : 89.27 % 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: -0.42 (0.23), residues: 1360 helix: 0.52 (0.24), residues: 425 sheet: 0.58 (0.25), residues: 480 loop : -1.99 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 206 HIS 0.004 0.001 HIS C 177 PHE 0.013 0.002 PHE B 236 TYR 0.014 0.001 TYR C 248 ARG 0.004 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.419 Fit side-chains REVERT: B 129 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7155 (mt-10) REVERT: B 236 PHE cc_start: 0.7385 (m-80) cc_final: 0.7102 (m-80) REVERT: C 97 ASP cc_start: 0.7881 (p0) cc_final: 0.7312 (p0) REVERT: D 60 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8261 (p0) REVERT: D 172 ASP cc_start: 0.8069 (m-30) cc_final: 0.7737 (m-30) REVERT: D 236 PHE cc_start: 0.7139 (m-80) cc_final: 0.6842 (m-80) REVERT: D 255 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7920 (mtt90) outliers start: 12 outliers final: 8 residues processed: 190 average time/residue: 0.2458 time to fit residues: 65.6097 Evaluate side-chains 159 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 122 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 169 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11585 Z= 0.162 Angle : 0.516 8.498 15790 Z= 0.260 Chirality : 0.046 0.142 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.120 14.581 1510 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.45 % Allowed : 12.50 % Favored : 86.05 % 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: -0.11 (0.23), residues: 1360 helix: 0.96 (0.25), residues: 420 sheet: 1.22 (0.27), residues: 390 loop : -1.95 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.008 0.001 PHE B 116 TYR 0.017 0.001 TYR D 245 ARG 0.003 0.000 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.286 Fit side-chains REVERT: B 129 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 245 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7509 (t80) REVERT: C 245 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7255 (t80) REVERT: D 60 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8370 (p0) REVERT: D 172 ASP cc_start: 0.8037 (m-30) cc_final: 0.7723 (m-30) outliers start: 18 outliers final: 13 residues processed: 178 average time/residue: 0.2215 time to fit residues: 56.9894 Evaluate side-chains 169 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 215 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 60 ASN D 60 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11585 Z= 0.190 Angle : 0.508 7.717 15790 Z= 0.256 Chirality : 0.046 0.140 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.035 14.670 1510 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.94 % Allowed : 14.84 % Favored : 83.23 % 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: -0.05 (0.23), residues: 1360 helix: 1.08 (0.25), residues: 420 sheet: 1.19 (0.27), residues: 390 loop : -1.92 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.002 0.001 HIS B 169 PHE 0.010 0.001 PHE E 236 TYR 0.017 0.001 TYR D 245 ARG 0.004 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.359 Fit side-chains REVERT: B 114 MET cc_start: 0.8396 (ttm) cc_final: 0.8115 (ttm) REVERT: B 245 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 245 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7232 (t80) REVERT: D 172 ASP cc_start: 0.8019 (m-30) cc_final: 0.7701 (m-30) REVERT: D 233 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6628 (tt0) outliers start: 24 outliers final: 14 residues processed: 179 average time/residue: 0.2249 time to fit residues: 58.1390 Evaluate side-chains 166 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 0.0010 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 0.0570 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 169 HIS ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11585 Z= 0.127 Angle : 0.475 6.512 15790 Z= 0.238 Chirality : 0.045 0.138 1740 Planarity : 0.003 0.022 2005 Dihedral : 3.848 13.858 1510 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.94 % Allowed : 14.92 % Favored : 83.15 % 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: 0.03 (0.23), residues: 1360 helix: 1.17 (0.25), residues: 420 sheet: 1.21 (0.27), residues: 390 loop : -1.87 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.007 0.001 PHE E 236 TYR 0.015 0.001 TYR D 245 ARG 0.004 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.260 Fit side-chains REVERT: A 245 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7033 (t80) REVERT: B 239 MET cc_start: 0.7125 (tpp) cc_final: 0.6819 (ttp) REVERT: B 245 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 245 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7238 (t80) REVERT: D 172 ASP cc_start: 0.8013 (m-30) cc_final: 0.7715 (m-30) outliers start: 24 outliers final: 14 residues processed: 177 average time/residue: 0.2167 time to fit residues: 55.9237 Evaluate side-chains 163 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 136 ASN C 139 GLN D 21 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 11585 Z= 0.491 Angle : 0.638 6.894 15790 Z= 0.325 Chirality : 0.051 0.142 1740 Planarity : 0.003 0.021 2005 Dihedral : 4.590 17.093 1510 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.58 % Allowed : 15.16 % Favored : 82.26 % 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: -0.25 (0.23), residues: 1360 helix: 0.85 (0.26), residues: 425 sheet: 0.96 (0.27), residues: 390 loop : -1.90 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 206 HIS 0.005 0.002 HIS C 177 PHE 0.010 0.002 PHE A 133 TYR 0.021 0.002 TYR D 245 ARG 0.005 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.339 Fit side-chains REVERT: A 60 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8369 (p0) REVERT: A 233 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: A 245 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 245 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.6630 (t80) REVERT: C 233 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6295 (tt0) REVERT: C 245 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6789 (t80) REVERT: D 172 ASP cc_start: 0.8022 (m-30) cc_final: 0.7745 (m-30) REVERT: D 233 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: D 245 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7462 (t80) REVERT: D 255 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8089 (mtt90) REVERT: E 233 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: E 245 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.6639 (t80) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.2509 time to fit residues: 65.9699 Evaluate side-chains 179 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 89 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11585 Z= 0.234 Angle : 0.536 6.376 15790 Z= 0.270 Chirality : 0.047 0.138 1740 Planarity : 0.003 0.030 2005 Dihedral : 4.235 16.555 1510 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.50 % Allowed : 16.53 % Favored : 80.97 % 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: -0.22 (0.23), residues: 1360 helix: 0.99 (0.25), residues: 420 sheet: 0.97 (0.27), residues: 390 loop : -1.97 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 206 HIS 0.003 0.001 HIS B 177 PHE 0.017 0.001 PHE E 236 TYR 0.017 0.001 TYR D 245 ARG 0.006 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6880 (t80) REVERT: B 245 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6816 (t80) REVERT: C 21 ASN cc_start: 0.8507 (t0) cc_final: 0.8263 (t160) REVERT: C 233 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6311 (tt0) REVERT: C 245 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6924 (t80) REVERT: D 172 ASP cc_start: 0.8020 (m-30) cc_final: 0.7741 (m-30) REVERT: D 245 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7438 (t80) REVERT: D 255 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8018 (mtt90) REVERT: E 245 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6431 (t80) outliers start: 31 outliers final: 21 residues processed: 166 average time/residue: 0.2510 time to fit residues: 58.4495 Evaluate side-chains 165 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 11585 Z= 0.498 Angle : 0.650 6.451 15790 Z= 0.332 Chirality : 0.051 0.141 1740 Planarity : 0.003 0.025 2005 Dihedral : 4.685 17.886 1510 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.58 % Allowed : 16.85 % Favored : 80.56 % 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: -0.44 (0.23), residues: 1360 helix: 0.62 (0.25), residues: 425 sheet: 0.71 (0.25), residues: 455 loop : -2.16 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 206 HIS 0.005 0.002 HIS A 177 PHE 0.010 0.002 PHE A 116 TYR 0.021 0.002 TYR D 245 ARG 0.006 0.001 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.285 Fit side-chains REVERT: A 233 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: A 245 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.6762 (t80) REVERT: B 114 MET cc_start: 0.8477 (ttm) cc_final: 0.7957 (ttm) REVERT: B 245 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.6626 (t80) REVERT: C 233 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6178 (tt0) REVERT: C 245 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6764 (t80) REVERT: D 172 ASP cc_start: 0.8014 (m-30) cc_final: 0.7746 (m-30) REVERT: D 233 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6245 (tt0) REVERT: D 245 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7298 (t80) REVERT: D 255 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.8089 (mtt90) REVERT: E 233 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: E 245 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6374 (t80) outliers start: 32 outliers final: 23 residues processed: 178 average time/residue: 0.2553 time to fit residues: 63.0899 Evaluate side-chains 166 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11585 Z= 0.222 Angle : 0.543 6.514 15790 Z= 0.274 Chirality : 0.047 0.139 1740 Planarity : 0.003 0.040 2005 Dihedral : 4.265 17.252 1510 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.82 % Allowed : 17.26 % Favored : 79.92 % 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: -0.39 (0.23), residues: 1360 helix: 0.87 (0.25), residues: 420 sheet: 0.84 (0.27), residues: 390 loop : -2.06 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 206 HIS 0.003 0.001 HIS B 177 PHE 0.010 0.001 PHE B 116 TYR 0.017 0.001 TYR D 245 ARG 0.007 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.381 Fit side-chains REVERT: A 233 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 245 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 114 MET cc_start: 0.8419 (ttm) cc_final: 0.7888 (ttm) REVERT: B 245 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.6620 (t80) REVERT: C 21 ASN cc_start: 0.8493 (t0) cc_final: 0.8221 (t0) REVERT: C 233 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6177 (tt0) REVERT: C 245 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6687 (t80) REVERT: D 172 ASP cc_start: 0.8018 (m-30) cc_final: 0.7733 (m-30) REVERT: D 233 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6283 (tt0) REVERT: D 245 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7335 (t80) REVERT: D 255 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8020 (mtt90) REVERT: E 233 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: E 236 PHE cc_start: 0.7142 (m-80) cc_final: 0.6821 (m-80) REVERT: E 245 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6332 (t80) outliers start: 35 outliers final: 23 residues processed: 175 average time/residue: 0.2465 time to fit residues: 60.4155 Evaluate side-chains 168 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS C 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11585 Z= 0.167 Angle : 0.514 7.155 15790 Z= 0.257 Chirality : 0.046 0.138 1740 Planarity : 0.003 0.038 2005 Dihedral : 3.956 16.362 1510 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.66 % Allowed : 17.98 % Favored : 79.35 % 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: -0.25 (0.23), residues: 1360 helix: 0.98 (0.25), residues: 420 sheet: 1.10 (0.27), residues: 380 loop : -2.06 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.009 0.001 PHE C 106 TYR 0.015 0.001 TYR B 245 ARG 0.008 0.000 ARG E 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.146 Fit side-chains REVERT: A 233 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6487 (tt0) REVERT: A 236 PHE cc_start: 0.7164 (m-80) cc_final: 0.6962 (m-80) REVERT: A 245 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6869 (t80) REVERT: B 245 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.6722 (t80) REVERT: C 233 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6162 (tt0) REVERT: C 245 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6669 (t80) REVERT: D 172 ASP cc_start: 0.8026 (m-30) cc_final: 0.7713 (m-30) REVERT: D 233 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6159 (tt0) REVERT: D 245 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7386 (t80) REVERT: D 255 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.8006 (mtt90) REVERT: E 233 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: E 245 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6422 (t80) outliers start: 33 outliers final: 22 residues processed: 174 average time/residue: 0.2319 time to fit residues: 57.6465 Evaluate side-chains 174 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0370 chunk 32 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 0.0020 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** E 233 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 = 0.3552 r_free = 0.3552 target = 0.145025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111911 restraints weight = 12484.113| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.00 r_work: 0.2996 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11585 Z= 0.177 Angle : 0.516 6.751 15790 Z= 0.258 Chirality : 0.046 0.136 1740 Planarity : 0.003 0.044 2005 Dihedral : 3.938 16.720 1510 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.82 % Allowed : 17.66 % Favored : 79.52 % 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: -0.21 (0.23), residues: 1360 helix: 1.02 (0.26), residues: 420 sheet: 1.11 (0.27), residues: 380 loop : -2.04 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.008 0.001 PHE C 106 TYR 0.014 0.001 TYR A 245 ARG 0.009 0.000 ARG E 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.78 seconds wall clock time: 44 minutes 57.68 seconds (2697.68 seconds total)