Starting phenix.real_space_refine on Sun Aug 4 18:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/08_2024/8twz_41673.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/08_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_41673/08_2024/8twz_41673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/08_2024/8twz_41673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/08_2024/8twz_41673.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/08_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-5409/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: 6.25, 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: 4.36 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: 1.44 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: 3.95 Time building geometry restraints manager: 4.70 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 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.329 3.040 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.330 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.330 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.340 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- 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 : 1.291 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: 0.2572 time to fit residues: 67.9999 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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: 0.9990 chunk 102 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 69 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 169 HIS B 233 GLN C 60 ASN C 89 ASN D 60 ASN D 89 ASN D 233 GLN E 60 ASN E 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11585 Z= 0.156 Angle : 0.511 5.937 15790 Z= 0.258 Chirality : 0.046 0.133 1740 Planarity : 0.003 0.020 2005 Dihedral : 4.134 14.964 1510 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.81 % Allowed : 7.74 % Favored : 91.45 % 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: -0.09 (0.23), residues: 1360 helix: 1.04 (0.24), residues: 395 sheet: 0.79 (0.27), residues: 445 loop : -1.73 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.001 0.001 HIS C 177 PHE 0.015 0.001 PHE B 236 TYR 0.010 0.001 TYR B 245 ARG 0.003 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 182 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.277 Fit side-chains REVERT: A 270 TYR cc_start: 0.7771 (m-10) cc_final: 0.7554 (m-80) REVERT: B 129 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 236 PHE cc_start: 0.7356 (m-80) cc_final: 0.7108 (m-80) REVERT: C 114 MET cc_start: 0.8499 (ttm) cc_final: 0.8251 (ttm) REVERT: C 174 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7650 (ttm-80) REVERT: D 97 ASP cc_start: 0.7792 (p0) cc_final: 0.7541 (p0) REVERT: D 150 GLU cc_start: 0.6168 (pt0) cc_final: 0.5880 (mt-10) REVERT: D 172 ASP cc_start: 0.8025 (m-30) cc_final: 0.7653 (m-30) REVERT: D 255 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7704 (mtt90) outliers start: 10 outliers final: 8 residues processed: 182 average time/residue: 0.2312 time to fit residues: 60.1337 Evaluate side-chains 152 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN 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: 9.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 122 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 98 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 169 HIS ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 60 ASN C 169 HIS D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11585 Z= 0.150 Angle : 0.504 7.361 15790 Z= 0.252 Chirality : 0.046 0.145 1740 Planarity : 0.003 0.023 2005 Dihedral : 3.853 12.015 1510 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.21 % Allowed : 9.76 % 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: 0.29 (0.23), residues: 1360 helix: 1.41 (0.25), residues: 395 sheet: 1.38 (0.27), residues: 415 loop : -1.75 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS B 169 PHE 0.017 0.001 PHE E 236 TYR 0.013 0.001 TYR C 245 ARG 0.003 0.000 ARG B 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 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.103 Fit side-chains REVERT: A 215 ILE cc_start: 0.7389 (mm) cc_final: 0.7149 (mt) REVERT: B 129 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7180 (mt-10) REVERT: C 34 LYS cc_start: 0.8348 (mttp) cc_final: 0.8068 (mttt) REVERT: C 114 MET cc_start: 0.8489 (ttm) cc_final: 0.8213 (ttm) REVERT: C 174 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7592 (tpp-160) REVERT: C 245 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7254 (t80) REVERT: D 97 ASP cc_start: 0.7913 (p0) cc_final: 0.7402 (p0) REVERT: D 150 GLU cc_start: 0.6189 (pt0) cc_final: 0.5883 (mt-10) REVERT: D 172 ASP cc_start: 0.8000 (m-30) cc_final: 0.7667 (m-30) REVERT: D 236 PHE cc_start: 0.7148 (m-80) cc_final: 0.6784 (m-80) REVERT: E 30 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6709 (mt-10) outliers start: 15 outliers final: 9 residues processed: 182 average time/residue: 0.2350 time to fit residues: 60.8446 Evaluate side-chains 162 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B 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 245 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 60 ASN D 27 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1637 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= 0.189 Angle : 0.505 7.515 15790 Z= 0.254 Chirality : 0.046 0.146 1740 Planarity : 0.003 0.023 2005 Dihedral : 3.847 12.572 1510 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.29 % Allowed : 12.02 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1360 helix: 1.57 (0.25), residues: 395 sheet: 1.40 (0.27), residues: 415 loop : -1.70 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS C 177 PHE 0.010 0.001 PHE E 236 TYR 0.013 0.001 TYR B 245 ARG 0.003 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 183 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.190 Fit side-chains REVERT: B 114 MET cc_start: 0.8501 (ttm) cc_final: 0.7984 (ttm) REVERT: B 239 MET cc_start: 0.7167 (tpp) cc_final: 0.6873 (ttp) REVERT: B 245 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7361 (t80) REVERT: C 34 LYS cc_start: 0.8372 (mttp) cc_final: 0.8091 (mttt) REVERT: C 114 MET cc_start: 0.8464 (ttm) cc_final: 0.8218 (ttm) REVERT: C 245 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7168 (t80) REVERT: D 97 ASP cc_start: 0.8029 (p0) cc_final: 0.7503 (p0) REVERT: D 150 GLU cc_start: 0.6233 (pt0) cc_final: 0.5809 (mt-10) REVERT: D 172 ASP cc_start: 0.8010 (m-30) cc_final: 0.7696 (m-30) REVERT: E 215 ILE cc_start: 0.7425 (mm) cc_final: 0.7199 (mt) outliers start: 16 outliers final: 10 residues processed: 179 average time/residue: 0.2234 time to fit residues: 57.0883 Evaluate side-chains 156 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 ASN 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 E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 60 ASN C 60 ASN D 21 ASN D 27 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11585 Z= 0.301 Angle : 0.557 8.727 15790 Z= 0.282 Chirality : 0.049 0.155 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.058 14.117 1510 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 85.00 % 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: 0.29 (0.23), residues: 1360 helix: 1.51 (0.25), residues: 395 sheet: 1.26 (0.27), residues: 415 loop : -1.73 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.003 0.001 HIS C 177 PHE 0.016 0.001 PHE E 236 TYR 0.015 0.001 TYR D 245 ARG 0.003 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 186 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.239 Fit side-chains REVERT: B 107 LEU cc_start: 0.8516 (tt) cc_final: 0.8302 (tt) REVERT: B 114 MET cc_start: 0.8522 (ttm) cc_final: 0.8064 (ttm) REVERT: B 239 MET cc_start: 0.7204 (tpp) cc_final: 0.6883 (ttp) REVERT: B 245 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7253 (t80) REVERT: C 34 LYS cc_start: 0.8440 (mttp) cc_final: 0.8143 (mttt) REVERT: C 114 MET cc_start: 0.8439 (ttm) cc_final: 0.8202 (ttm) REVERT: C 245 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7203 (t80) REVERT: D 172 ASP cc_start: 0.8034 (m-30) cc_final: 0.7753 (m-30) REVERT: E 30 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: E 215 ILE cc_start: 0.7519 (mm) cc_final: 0.7309 (mt) outliers start: 31 outliers final: 16 residues processed: 182 average time/residue: 0.2622 time to fit residues: 65.9408 Evaluate side-chains 163 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 215 ILE 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 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 240 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11585 Z= 0.215 Angle : 0.525 7.482 15790 Z= 0.264 Chirality : 0.047 0.138 1740 Planarity : 0.003 0.025 2005 Dihedral : 3.990 14.207 1510 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.29 % Allowed : 14.76 % Favored : 83.95 % 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: 0.23 (0.23), residues: 1360 helix: 1.57 (0.25), residues: 390 sheet: 1.18 (0.27), residues: 415 loop : -1.79 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.003 0.001 HIS B 177 PHE 0.024 0.001 PHE E 236 TYR 0.017 0.001 TYR A 245 ARG 0.005 0.000 ARG C 123 *********************** 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 161 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.315 Fit side-chains REVERT: B 114 MET cc_start: 0.8519 (ttm) cc_final: 0.8059 (ttm) REVERT: B 239 MET cc_start: 0.7171 (tpp) cc_final: 0.6838 (ttp) REVERT: B 245 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 34 LYS cc_start: 0.8423 (mttp) cc_final: 0.8131 (mttt) REVERT: C 245 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6998 (t80) REVERT: D 172 ASP cc_start: 0.8020 (m-30) cc_final: 0.7712 (m-30) REVERT: E 30 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: E 215 ILE cc_start: 0.7525 (mm) cc_final: 0.7321 (mt) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.2653 time to fit residues: 57.3416 Evaluate side-chains 157 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 56 LEU 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11585 Z= 0.186 Angle : 0.512 6.879 15790 Z= 0.257 Chirality : 0.047 0.137 1740 Planarity : 0.003 0.033 2005 Dihedral : 3.904 13.806 1510 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.77 % Allowed : 15.16 % Favored : 83.06 % 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 (0.24), residues: 1360 helix: 1.64 (0.25), residues: 390 sheet: 1.15 (0.27), residues: 415 loop : -1.78 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.020 0.001 PHE E 236 TYR 0.016 0.001 TYR A 245 ARG 0.007 0.000 ARG E 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 172 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 114 MET cc_start: 0.8501 (ttm) cc_final: 0.7998 (ttm) REVERT: B 239 MET cc_start: 0.7208 (tpp) cc_final: 0.6896 (ttp) REVERT: B 245 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 34 LYS cc_start: 0.8434 (mttp) cc_final: 0.8153 (mttt) REVERT: C 123 ARG cc_start: 0.7103 (mtp85) cc_final: 0.6868 (mtp-110) REVERT: C 245 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7099 (t80) REVERT: D 172 ASP cc_start: 0.8037 (m-30) cc_final: 0.7761 (m-30) REVERT: D 255 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.8009 (mtt90) REVERT: E 30 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6814 (mt-10) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.2609 time to fit residues: 59.8313 Evaluate side-chains 161 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER 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 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 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 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 240 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 0.0570 chunk 124 optimal weight: 6.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 169 HIS D 21 ASN D 233 GLN E 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11585 Z= 0.164 Angle : 0.516 8.699 15790 Z= 0.259 Chirality : 0.046 0.146 1740 Planarity : 0.003 0.038 2005 Dihedral : 3.819 13.411 1510 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.69 % Allowed : 15.65 % Favored : 82.66 % 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: 0.28 (0.24), residues: 1360 helix: 1.64 (0.25), residues: 390 sheet: 1.15 (0.27), residues: 415 loop : -1.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.002 0.001 HIS A 177 PHE 0.019 0.001 PHE E 236 TYR 0.015 0.001 TYR A 245 ARG 0.008 0.000 ARG E 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 169 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.6829 (t80) REVERT: B 239 MET cc_start: 0.7181 (tpp) cc_final: 0.6857 (ttp) REVERT: B 245 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7267 (t80) REVERT: C 34 LYS cc_start: 0.8426 (mttp) cc_final: 0.8142 (mttt) REVERT: C 123 ARG cc_start: 0.7079 (mtp85) cc_final: 0.6875 (mtp-110) REVERT: C 245 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7114 (t80) REVERT: D 172 ASP cc_start: 0.8005 (m-30) cc_final: 0.7740 (m-30) REVERT: D 233 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6017 (tt0) REVERT: D 255 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7977 (mtt90) REVERT: E 30 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6741 (mt-10) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 0.2619 time to fit residues: 58.9823 Evaluate side-chains 160 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER 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 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 D residue 233 GLN Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 SER 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: 1.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11585 Z= 0.197 Angle : 0.528 8.239 15790 Z= 0.264 Chirality : 0.047 0.135 1740 Planarity : 0.003 0.043 2005 Dihedral : 3.866 13.732 1510 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % 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: 0.26 (0.24), residues: 1360 helix: 1.58 (0.25), residues: 390 sheet: 1.15 (0.27), residues: 415 loop : -1.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS A 177 PHE 0.018 0.001 PHE E 236 TYR 0.018 0.001 TYR E 245 ARG 0.009 0.000 ARG E 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 164 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 239 MET cc_start: 0.7261 (tpp) cc_final: 0.6925 (ttp) REVERT: B 245 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7255 (t80) REVERT: C 34 LYS cc_start: 0.8417 (mttp) cc_final: 0.8144 (mttt) REVERT: C 123 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6892 (mtp-110) REVERT: C 245 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7120 (t80) REVERT: D 172 ASP cc_start: 0.8014 (m-30) cc_final: 0.7744 (m-30) REVERT: D 236 PHE cc_start: 0.7139 (m-10) cc_final: 0.6724 (m-80) REVERT: D 255 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.8000 (mtt90) REVERT: E 30 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6767 (mt-10) outliers start: 22 outliers final: 16 residues processed: 158 average time/residue: 0.2639 time to fit residues: 57.4168 Evaluate side-chains 161 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE 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 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11585 Z= 0.138 Angle : 0.505 7.988 15790 Z= 0.252 Chirality : 0.046 0.135 1740 Planarity : 0.003 0.039 2005 Dihedral : 3.712 13.541 1510 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.45 % Allowed : 16.37 % Favored : 82.18 % 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: 0.33 (0.24), residues: 1360 helix: 1.64 (0.25), residues: 390 sheet: 1.20 (0.27), residues: 415 loop : -1.69 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 206 HIS 0.002 0.001 HIS A 177 PHE 0.022 0.001 PHE E 236 TYR 0.016 0.001 TYR E 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 176 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 236 PHE cc_start: 0.7133 (m-80) cc_final: 0.6888 (m-80) REVERT: A 245 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 61 THR cc_start: 0.7778 (t) cc_final: 0.7562 (p) REVERT: B 239 MET cc_start: 0.7106 (tpp) cc_final: 0.6818 (ttp) REVERT: B 245 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 34 LYS cc_start: 0.8379 (mttp) cc_final: 0.8130 (mttt) REVERT: C 107 LEU cc_start: 0.8319 (tt) cc_final: 0.7900 (tp) REVERT: C 123 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6821 (mtp-110) REVERT: C 245 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7122 (t80) REVERT: D 172 ASP cc_start: 0.8010 (m-30) cc_final: 0.7761 (m-30) REVERT: D 255 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7934 (mtt90) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 0.2547 time to fit residues: 60.4879 Evaluate side-chains 155 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER 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 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE 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 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 15 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.117448 restraints weight = 12384.929| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3239 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11585 Z= 0.132 Angle : 0.502 7.320 15790 Z= 0.249 Chirality : 0.046 0.130 1740 Planarity : 0.003 0.040 2005 Dihedral : 3.624 13.336 1510 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.21 % Allowed : 16.45 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1360 helix: 1.62 (0.25), residues: 395 sheet: 1.25 (0.27), residues: 415 loop : -1.60 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 206 HIS 0.002 0.001 HIS D 177 PHE 0.029 0.001 PHE E 236 TYR 0.013 0.001 TYR E 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: 2409.11 seconds wall clock time: 43 minutes 42.21 seconds (2622.21 seconds total)