Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 17:25:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/04_2023/6vxo_21446_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 24 5.16 5 C 5548 2.51 5 N 1184 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "E" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.57, per 1000 atoms: 0.57 Number of scatterers: 8048 At special positions: 0 Unit cell: (123.654, 123.654, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 12 15.00 O 1280 8.00 N 1184 7.00 C 5548 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: 3.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 24 through 44 removed outlier: 4.787A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 53 through 76 Processing helix chain 'A' and resid 88 through 105 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.587A pdb=" N LEU A 121 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG A 122 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 149 through 168 removed outlier: 3.665A pdb=" N MET A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 202 through 205 No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 209 through 237 removed outlier: 4.045A pdb=" N TRP A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 216 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 219 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY A 222 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 4.787A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 76 Processing helix chain 'C' and resid 88 through 105 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.588A pdb=" N LEU C 121 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG C 122 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 125 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 149 through 168 removed outlier: 3.664A pdb=" N MET C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 188 through 191 No H-bonds generated for 'chain 'C' and resid 188 through 191' Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 209 through 237 removed outlier: 4.045A pdb=" N TRP C 212 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 213 " --> pdb=" O TRP C 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 216 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL C 219 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 222 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL C 235 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 44 removed outlier: 4.787A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 53 through 76 Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.587A pdb=" N LEU D 121 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG D 122 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 125 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 149 through 168 removed outlier: 3.664A pdb=" N MET D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 202 through 205 No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 209 through 237 removed outlier: 4.045A pdb=" N TRP D 212 " --> pdb=" O PRO D 209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 213 " --> pdb=" O TRP D 210 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 216 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL D 219 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY D 222 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 235 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 44 removed outlier: 4.786A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 53 through 76 Processing helix chain 'E' and resid 88 through 105 Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.587A pdb=" N LEU E 121 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG E 122 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG E 125 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 149 through 168 removed outlier: 3.665A pdb=" N MET E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 188 through 191 No H-bonds generated for 'chain 'E' and resid 188 through 191' Processing helix chain 'E' and resid 202 through 205 No H-bonds generated for 'chain 'E' and resid 202 through 205' Processing helix chain 'E' and resid 209 through 237 removed outlier: 4.045A pdb=" N TRP E 212 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 213 " --> pdb=" O TRP E 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL E 216 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 219 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY E 222 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL E 235 " --> pdb=" O GLY E 232 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 888 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: 1.72 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1084 1.30 - 1.43: 2299 1.43 - 1.55: 4723 1.55 - 1.68: 90 1.68 - 1.80: 48 Bond restraints: 8244 Sorted by residual: bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV C 302 " pdb=" O31 POV C 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV A 303 " pdb=" O31 POV A 303 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.28e+01 ... (remaining 8239 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 168 106.62 - 113.48: 5012 113.48 - 120.33: 3033 120.33 - 127.19: 2807 127.19 - 134.04: 92 Bond angle restraints: 11112 Sorted by residual: angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 111.91 107.01 4.90 8.90e-01 1.26e+00 3.03e+01 angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL E 114 " pdb=" CA VAL E 114 " pdb=" C VAL E 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL D 114 " pdb=" CA VAL D 114 " pdb=" C VAL D 114 " ideal model delta sigma weight residual 111.91 107.04 4.87 8.90e-01 1.26e+00 3.00e+01 angle pdb=" O13 POV A 303 " pdb=" P POV A 303 " pdb=" O14 POV A 303 " ideal model delta sigma weight residual 121.11 109.49 11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 4051 24.08 - 48.16: 562 48.16 - 72.24: 159 72.24 - 96.32: 44 96.32 - 120.40: 12 Dihedral angle restraints: 4828 sinusoidal: 2160 harmonic: 2668 Sorted by residual: dihedral pdb=" CA VAL C 109 " pdb=" C VAL C 109 " pdb=" N GLU C 110 " pdb=" CA GLU C 110 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N ASN E 236 " pdb=" CA ASN E 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 235 " pdb=" C VAL D 235 " pdb=" N ASN D 236 " pdb=" CA ASN D 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 587 0.027 - 0.053: 338 0.053 - 0.079: 207 0.079 - 0.106: 93 0.106 - 0.132: 35 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA VAL A 235 " pdb=" N VAL A 235 " pdb=" C VAL A 235 " pdb=" CB VAL A 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 235 " pdb=" N VAL D 235 " pdb=" C VAL D 235 " pdb=" CB VAL D 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL C 235 " pdb=" N VAL C 235 " pdb=" C VAL C 235 " pdb=" CB VAL C 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1257 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE D 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE D 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE C 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 234 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ILE A 234 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 234 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 235 " -0.010 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 315 2.68 - 3.24: 8618 3.24 - 3.79: 12599 3.79 - 4.35: 15546 4.35 - 4.90: 25373 Nonbonded interactions: 62451 Sorted by model distance: nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 217 " model vdw 2.125 2.440 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 217 " model vdw 2.125 2.440 nonbonded pdb=" O TYR E 214 " pdb=" OG SER E 217 " model vdw 2.126 2.440 nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 217 " model vdw 2.126 2.440 nonbonded pdb=" O PHE E 161 " pdb=" OH TYR E 214 " model vdw 2.219 2.440 ... (remaining 62446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 240 or resid 301 through 302)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 240 or resid 301 through 302)) selection = (chain 'E' and (resid 15 through 240 or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.190 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.012 0.097 8244 Z= 0.766 Angle : 1.401 11.619 11112 Z= 0.585 Chirality : 0.047 0.132 1260 Planarity : 0.005 0.035 1272 Dihedral : 24.434 120.396 3084 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.17 % Favored : 87.39 % Rotamer Outliers : 21.57 % 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: -3.90 (0.24), residues: 896 helix: -1.88 (0.17), residues: 640 sheet: None (None), residues: 0 loop : -4.16 (0.33), residues: 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 207 time to evaluate : 0.928 Fit side-chains revert: symmetry clash outliers start: 176 outliers final: 141 residues processed: 336 average time/residue: 0.1489 time to fit residues: 71.9751 Evaluate side-chains 313 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 172 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 0 residues processed: 141 average time/residue: 0.0775 time to fit residues: 20.9883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 228 ASN A 237 ASN C 90 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 228 ASN C 237 ASN D 90 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 228 ASN D 237 ASN E 90 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN E 228 ASN E 237 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8244 Z= 0.204 Angle : 0.649 6.051 11112 Z= 0.327 Chirality : 0.043 0.181 1260 Planarity : 0.004 0.019 1272 Dihedral : 21.783 106.251 1416 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.28), residues: 896 helix: -0.10 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.12 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 0.960 Fit side-chains outliers start: 27 outliers final: 8 residues processed: 258 average time/residue: 0.1596 time to fit residues: 59.0376 Evaluate side-chains 209 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0713 time to fit residues: 2.2169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8244 Z= 0.181 Angle : 0.663 7.557 11112 Z= 0.327 Chirality : 0.045 0.220 1260 Planarity : 0.004 0.019 1272 Dihedral : 20.155 99.787 1416 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer Outliers : 4.66 % 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: -0.94 (0.29), residues: 896 helix: 0.28 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -2.57 (0.38), residues: 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 0.976 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 253 average time/residue: 0.1456 time to fit residues: 54.2462 Evaluate side-chains 226 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1042 time to fit residues: 4.1231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 53 optimal weight: 0.0470 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8244 Z= 0.167 Angle : 0.641 10.665 11112 Z= 0.321 Chirality : 0.042 0.158 1260 Planarity : 0.004 0.026 1272 Dihedral : 18.602 89.202 1416 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 4.90 % 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: -0.66 (0.29), residues: 896 helix: 0.32 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.11 (0.38), residues: 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 268 average time/residue: 0.1534 time to fit residues: 59.3913 Evaluate side-chains 221 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0767 time to fit residues: 3.2747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8244 Z= 0.186 Angle : 0.707 12.360 11112 Z= 0.341 Chirality : 0.043 0.217 1260 Planarity : 0.004 0.028 1272 Dihedral : 17.671 84.136 1416 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 896 helix: 0.31 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 26 residues processed: 233 average time/residue: 0.1546 time to fit residues: 52.3033 Evaluate side-chains 233 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1022 time to fit residues: 5.5576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8244 Z= 0.205 Angle : 0.682 12.790 11112 Z= 0.341 Chirality : 0.042 0.168 1260 Planarity : 0.004 0.028 1272 Dihedral : 16.901 81.126 1416 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer Outliers : 1.72 % 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: -0.47 (0.29), residues: 896 helix: 0.31 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.74 (0.39), residues: 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 221 average time/residue: 0.1575 time to fit residues: 50.3986 Evaluate side-chains 208 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1288 time to fit residues: 2.3651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8244 Z= 0.178 Angle : 0.682 13.091 11112 Z= 0.337 Chirality : 0.043 0.208 1260 Planarity : 0.004 0.026 1272 Dihedral : 15.956 73.901 1416 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 2.57 % 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: -0.46 (0.29), residues: 896 helix: 0.31 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -1.83 (0.40), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 0.978 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 228 average time/residue: 0.1647 time to fit residues: 53.4409 Evaluate side-chains 210 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0834 time to fit residues: 2.5224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8244 Z= 0.183 Angle : 0.707 12.334 11112 Z= 0.348 Chirality : 0.044 0.274 1260 Planarity : 0.004 0.040 1272 Dihedral : 15.475 71.491 1416 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer Outliers : 1.59 % 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: -0.46 (0.29), residues: 896 helix: 0.31 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.73 (0.39), residues: 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 0.937 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 220 average time/residue: 0.1639 time to fit residues: 51.2321 Evaluate side-chains 211 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0783 time to fit residues: 2.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8244 Z= 0.225 Angle : 0.733 12.315 11112 Z= 0.363 Chirality : 0.045 0.252 1260 Planarity : 0.005 0.036 1272 Dihedral : 15.467 72.841 1416 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.29), residues: 896 helix: 0.33 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 0.935 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 209 average time/residue: 0.1644 time to fit residues: 49.0763 Evaluate side-chains 194 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0797 time to fit residues: 1.7195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8244 Z= 0.188 Angle : 0.731 13.590 11112 Z= 0.358 Chirality : 0.046 0.316 1260 Planarity : 0.004 0.033 1272 Dihedral : 14.775 70.904 1416 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 0.37 % 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: -0.48 (0.28), residues: 896 helix: 0.34 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.911 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 207 average time/residue: 0.1639 time to fit residues: 48.3878 Evaluate side-chains 198 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0764 time to fit residues: 1.4787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097452 restraints weight = 15353.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100773 restraints weight = 6743.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102917 restraints weight = 4168.857| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 8244 Z= 0.233 Angle : 0.750 12.833 11112 Z= 0.371 Chirality : 0.046 0.301 1260 Planarity : 0.004 0.032 1272 Dihedral : 14.751 71.313 1416 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 896 helix: 0.26 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 256 =============================================================================== Job complete usr+sys time: 1713.32 seconds wall clock time: 31 minutes 40.30 seconds (1900.30 seconds total)