Starting phenix.real_space_refine on Mon Mar 11 10:34:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/03_2024/6vxo_21446_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/03_2024/6vxo_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_21446/03_2024/6vxo_21446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/03_2024/6vxo_21446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/03_2024/6vxo_21446_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/03_2024/6vxo_21446_updated.pdb" } resolution = 3.5 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= 0.003 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-dev-5265/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: 4.70, per 1000 atoms: 0.58 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: 3.20 Conformation dependent library (CDL) restraints added in 1.3 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: 1.41 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: 1.82 Time building geometry restraints manager: 3.44 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: 4071 24.08 - 48.16: 594 48.16 - 72.24: 175 72.24 - 96.32: 48 96.32 - 120.40: 12 Dihedral angle restraints: 4900 sinusoidal: 2232 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 4897 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.490 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 24.580 Find NCS groups from input model: 0.530 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- 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 : 24.970 120.396 3156 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 % Allowed : 21.08 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 PHE 0.017 0.002 PHE C 205 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG E 122 *********************** 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 : 0.990 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8605 (m-80) cc_final: 0.8347 (m-80) REVERT: A 47 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: A 54 TRP cc_start: 0.7193 (p-90) cc_final: 0.6970 (p-90) REVERT: A 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 65 TRP cc_start: 0.8015 (m100) cc_final: 0.7668 (t-100) REVERT: A 70 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8263 (tp30) REVERT: A 103 GLU cc_start: 0.8881 (tp30) cc_final: 0.8587 (tp30) REVERT: A 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 45 TYR cc_start: 0.8575 (m-80) cc_final: 0.8319 (m-80) REVERT: C 47 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (ttm-80) REVERT: C 54 TRP cc_start: 0.7194 (p-90) cc_final: 0.6965 (p-90) REVERT: C 63 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9140 (mm) REVERT: C 65 TRP cc_start: 0.8002 (m100) cc_final: 0.7624 (t-100) REVERT: C 70 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8243 (tp30) REVERT: C 103 GLU cc_start: 0.8868 (tp30) cc_final: 0.8620 (tp30) REVERT: C 115 LEU cc_start: 0.8801 (mt) cc_final: 0.8526 (mt) REVERT: C 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7598 (t80) REVERT: D 45 TYR cc_start: 0.8603 (m-80) cc_final: 0.8339 (m-80) REVERT: D 47 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: D 54 TRP cc_start: 0.7218 (p-90) cc_final: 0.6990 (p-90) REVERT: D 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 65 TRP cc_start: 0.7986 (m100) cc_final: 0.7618 (t-100) REVERT: D 70 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8265 (tp30) REVERT: D 103 GLU cc_start: 0.8885 (tp30) cc_final: 0.8677 (tp30) REVERT: D 115 LEU cc_start: 0.8844 (mt) cc_final: 0.8593 (mt) REVERT: D 230 PHE cc_start: 0.7821 (t80) cc_final: 0.7598 (t80) REVERT: E 45 TYR cc_start: 0.8632 (m-80) cc_final: 0.8402 (m-80) REVERT: E 47 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (ttm-80) REVERT: E 54 TRP cc_start: 0.7227 (p-90) cc_final: 0.7024 (p-90) REVERT: E 63 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (mm) REVERT: E 65 TRP cc_start: 0.8109 (m100) cc_final: 0.7658 (t-100) REVERT: E 70 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8274 (tp30) REVERT: E 115 LEU cc_start: 0.8688 (mt) cc_final: 0.8449 (mt) REVERT: E 230 PHE cc_start: 0.7851 (t80) cc_final: 0.7623 (t80) outliers start: 176 outliers final: 141 residues processed: 336 average time/residue: 0.1509 time to fit residues: 73.2220 Evaluate side-chains 329 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 180 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 237 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 237 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 237 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 237 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8244 Z= 0.176 Angle : 0.604 5.677 11112 Z= 0.311 Chirality : 0.040 0.149 1260 Planarity : 0.004 0.019 1272 Dihedral : 23.585 107.817 1756 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 11.03 % Allowed : 24.26 % Favored : 64.71 % 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: -1.60 (0.28), residues: 896 helix: -0.06 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 65 HIS 0.001 0.001 HIS C 52 PHE 0.013 0.001 PHE A 205 TYR 0.007 0.001 TYR C 49 ARG 0.001 0.000 ARG E 116 *********************** 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 318 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 228 time to evaluate : 0.899 Fit side-chains REVERT: A 43 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: A 45 TYR cc_start: 0.8497 (m-80) cc_final: 0.8273 (m-80) REVERT: A 54 TRP cc_start: 0.6886 (p-90) cc_final: 0.6680 (p-90) REVERT: A 65 TRP cc_start: 0.7936 (m100) cc_final: 0.7619 (t-100) REVERT: A 70 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8279 (tp30) REVERT: A 207 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 43 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (pp20) REVERT: C 45 TYR cc_start: 0.8451 (m-80) cc_final: 0.8226 (m-80) REVERT: C 54 TRP cc_start: 0.6900 (p-90) cc_final: 0.6674 (p-90) REVERT: C 65 TRP cc_start: 0.7926 (m100) cc_final: 0.7611 (t-100) REVERT: C 73 MET cc_start: 0.6485 (tpt) cc_final: 0.6269 (tpt) REVERT: C 147 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8722 (pp) REVERT: D 43 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: D 45 TYR cc_start: 0.8498 (m-80) cc_final: 0.8289 (m-80) REVERT: D 54 TRP cc_start: 0.6889 (p-90) cc_final: 0.6670 (p-90) REVERT: D 65 TRP cc_start: 0.7963 (m100) cc_final: 0.7613 (t-100) REVERT: D 93 ASP cc_start: 0.8754 (m-30) cc_final: 0.8435 (m-30) REVERT: D 138 ASP cc_start: 0.8160 (t0) cc_final: 0.7959 (t0) REVERT: D 147 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8723 (pp) REVERT: E 43 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: E 65 TRP cc_start: 0.8009 (m100) cc_final: 0.7659 (t-100) outliers start: 90 outliers final: 58 residues processed: 295 average time/residue: 0.1411 time to fit residues: 61.4138 Evaluate side-chains 274 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 210 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL 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: 0.9990 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.2052 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= 0.195 Angle : 0.645 11.179 11112 Z= 0.324 Chirality : 0.043 0.163 1260 Planarity : 0.004 0.020 1272 Dihedral : 22.425 109.778 1605 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 10.54 % Allowed : 28.31 % Favored : 61.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 896 helix: 0.35 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.001 0.000 HIS C 22 PHE 0.027 0.001 PHE C 94 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 119 *********************** 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 315 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 229 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8489 (m-80) cc_final: 0.8245 (m-80) REVERT: A 54 TRP cc_start: 0.6967 (p-90) cc_final: 0.6721 (p-90) REVERT: A 63 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 65 TRP cc_start: 0.7882 (m100) cc_final: 0.7676 (t-100) REVERT: A 73 MET cc_start: 0.6794 (tpt) cc_final: 0.6535 (tpt) REVERT: A 207 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7356 (mm-30) REVERT: C 45 TYR cc_start: 0.8492 (m-80) cc_final: 0.8263 (m-80) REVERT: C 54 TRP cc_start: 0.6987 (p-90) cc_final: 0.6785 (p-90) REVERT: C 63 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9180 (mm) REVERT: C 65 TRP cc_start: 0.7889 (m100) cc_final: 0.7543 (t-100) REVERT: C 147 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8718 (pp) REVERT: C 207 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 45 TYR cc_start: 0.8468 (m-80) cc_final: 0.8226 (m-80) REVERT: D 54 TRP cc_start: 0.6955 (p-90) cc_final: 0.6753 (p-90) REVERT: D 63 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9181 (mm) REVERT: D 65 TRP cc_start: 0.7865 (m100) cc_final: 0.7651 (t-100) REVERT: D 101 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9079 (mm) REVERT: D 207 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7328 (mm-30) REVERT: E 63 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9165 (mm) REVERT: E 65 TRP cc_start: 0.7952 (m100) cc_final: 0.7704 (t-100) REVERT: E 207 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7326 (mm-30) outliers start: 86 outliers final: 61 residues processed: 294 average time/residue: 0.1389 time to fit residues: 60.7976 Evaluate side-chains 276 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 209 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 90 ASN C 90 ASN D 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2407 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= 0.205 Angle : 0.626 7.723 11112 Z= 0.322 Chirality : 0.042 0.153 1260 Planarity : 0.004 0.026 1272 Dihedral : 21.327 104.132 1592 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 10.29 % Allowed : 27.70 % Favored : 62.01 % 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 (0.30), residues: 896 helix: 0.57 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -1.73 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.001 0.001 HIS C 171 PHE 0.027 0.001 PHE D 94 TYR 0.005 0.001 TYR D 45 ARG 0.001 0.000 ARG A 116 *********************** 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 301 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 217 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.6968 (p-90) cc_final: 0.6743 (p-90) REVERT: A 65 TRP cc_start: 0.7909 (m100) cc_final: 0.7579 (t-100) REVERT: A 73 MET cc_start: 0.6777 (tpt) cc_final: 0.6521 (tpt) REVERT: A 207 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 45 TYR cc_start: 0.8437 (m-80) cc_final: 0.8167 (m-80) REVERT: C 65 TRP cc_start: 0.7922 (m100) cc_final: 0.7590 (t-100) REVERT: C 73 MET cc_start: 0.6695 (tpt) cc_final: 0.6492 (tpt) REVERT: C 147 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8711 (pp) REVERT: C 207 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7373 (mm-30) REVERT: D 65 TRP cc_start: 0.7932 (m100) cc_final: 0.7572 (t-100) REVERT: D 101 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9124 (mm) REVERT: D 207 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7362 (mm-30) REVERT: E 65 TRP cc_start: 0.7908 (m100) cc_final: 0.7560 (t-100) REVERT: E 207 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7354 (mm-30) outliers start: 84 outliers final: 69 residues processed: 276 average time/residue: 0.1406 time to fit residues: 57.2735 Evaluate side-chains 281 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 210 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 36 ASN E 36 ASN E 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8244 Z= 0.168 Angle : 0.694 13.069 11112 Z= 0.331 Chirality : 0.042 0.162 1260 Planarity : 0.004 0.028 1272 Dihedral : 20.138 103.232 1586 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 9.31 % Allowed : 31.50 % Favored : 59.19 % 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: -0.30 (0.29), residues: 896 helix: 0.45 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 65 HIS 0.001 0.000 HIS C 22 PHE 0.024 0.001 PHE D 94 TYR 0.005 0.001 TYR A 49 ARG 0.001 0.000 ARG E 119 *********************** 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 287 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 211 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.6927 (p-90) cc_final: 0.6381 (p-90) REVERT: A 63 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 101 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 207 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7446 (mm-30) REVERT: C 43 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: C 45 TYR cc_start: 0.8399 (m-80) cc_final: 0.8145 (m-80) REVERT: C 54 TRP cc_start: 0.6767 (p-90) cc_final: 0.6395 (p-90) REVERT: C 63 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9109 (mm) REVERT: C 101 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9103 (mm) REVERT: C 147 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (pp) REVERT: C 207 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7348 (mm-30) REVERT: D 54 TRP cc_start: 0.6782 (p-90) cc_final: 0.6399 (p-90) REVERT: D 63 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9100 (mm) REVERT: D 101 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9108 (mm) REVERT: D 207 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7339 (mm-30) REVERT: E 54 TRP cc_start: 0.6856 (p-90) cc_final: 0.6485 (p-90) REVERT: E 63 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9127 (mm) REVERT: E 101 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9155 (mm) REVERT: E 207 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7444 (mm-30) outliers start: 76 outliers final: 54 residues processed: 267 average time/residue: 0.1500 time to fit residues: 58.3208 Evaluate side-chains 265 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN C 79 ASN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8244 Z= 0.213 Angle : 0.691 10.448 11112 Z= 0.335 Chirality : 0.043 0.170 1260 Planarity : 0.004 0.028 1272 Dihedral : 19.497 107.230 1560 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 8.70 % Allowed : 33.70 % Favored : 57.60 % 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: -0.34 (0.29), residues: 896 helix: 0.50 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 54 HIS 0.001 0.001 HIS C 171 PHE 0.020 0.001 PHE D 94 TYR 0.004 0.001 TYR C 45 ARG 0.001 0.000 ARG E 202 *********************** 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 274 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 203 time to evaluate : 0.863 Fit side-chains REVERT: A 63 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 207 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7500 (mm-30) REVERT: C 43 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7587 (pp20) REVERT: C 63 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9114 (mm) REVERT: C 147 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8752 (pp) REVERT: C 202 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8967 (mmt90) REVERT: C 207 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 63 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9105 (mm) REVERT: D 81 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8417 (mmmt) REVERT: D 101 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9113 (mm) REVERT: D 207 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7397 (mm-30) REVERT: E 63 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9108 (mm) REVERT: E 207 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7500 (mm-30) outliers start: 71 outliers final: 58 residues processed: 256 average time/residue: 0.1480 time to fit residues: 54.6614 Evaluate side-chains 260 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8244 Z= 0.165 Angle : 0.668 13.386 11112 Z= 0.326 Chirality : 0.042 0.169 1260 Planarity : 0.004 0.040 1272 Dihedral : 18.405 105.551 1558 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 9.07 % Allowed : 34.19 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 896 helix: 0.49 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.54 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 54 HIS 0.001 0.000 HIS D 22 PHE 0.019 0.001 PHE D 94 TYR 0.006 0.001 TYR C 49 ARG 0.001 0.000 ARG E 202 *********************** 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 282 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 208 time to evaluate : 0.946 Fit side-chains REVERT: A 63 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9173 (mm) REVERT: A 101 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9112 (mm) REVERT: A 201 MET cc_start: 0.8183 (ttp) cc_final: 0.7950 (ttm) REVERT: A 207 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 63 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9120 (mm) REVERT: C 81 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8405 (mmmt) REVERT: C 147 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8728 (pp) REVERT: C 202 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8951 (mmt90) REVERT: C 207 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7444 (mm-30) REVERT: D 63 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9118 (mm) REVERT: D 81 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8433 (mmmt) REVERT: D 101 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9140 (mm) REVERT: D 202 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8941 (mmt90) REVERT: D 207 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7432 (mm-30) REVERT: E 60 ASP cc_start: 0.8711 (t70) cc_final: 0.8081 (t0) REVERT: E 63 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9120 (mm) REVERT: E 81 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8459 (mmmt) REVERT: E 207 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7435 (mm-30) outliers start: 74 outliers final: 57 residues processed: 260 average time/residue: 0.1613 time to fit residues: 59.3065 Evaluate side-chains 270 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 ASN D 79 ASN D 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8244 Z= 0.175 Angle : 0.681 12.370 11112 Z= 0.333 Chirality : 0.042 0.172 1260 Planarity : 0.004 0.035 1272 Dihedral : 17.997 105.230 1552 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 8.58 % Allowed : 33.95 % Favored : 57.48 % 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: -0.14 (0.29), residues: 896 helix: 0.49 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 54 HIS 0.001 0.000 HIS A 22 PHE 0.017 0.001 PHE D 94 TYR 0.005 0.001 TYR C 49 ARG 0.001 0.000 ARG E 202 *********************** 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 277 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 0.939 Fit side-chains REVERT: A 63 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9179 (mm) REVERT: A 81 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8467 (mmmt) REVERT: A 101 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9087 (mm) REVERT: A 207 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7479 (mm-30) REVERT: C 43 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: C 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9127 (mm) REVERT: C 81 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8381 (mmmt) REVERT: C 147 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8709 (pp) REVERT: C 202 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8954 (mmt90) REVERT: C 207 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7463 (mm-30) REVERT: D 63 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9125 (mm) REVERT: D 81 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8361 (mmmt) REVERT: D 101 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9129 (mm) REVERT: D 202 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8959 (mmt90) REVERT: D 207 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7450 (mm-30) REVERT: E 60 ASP cc_start: 0.8704 (t70) cc_final: 0.8091 (t0) REVERT: E 63 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9156 (mm) REVERT: E 81 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8448 (mmmt) REVERT: E 207 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7412 (mm-30) outliers start: 70 outliers final: 57 residues processed: 255 average time/residue: 0.1607 time to fit residues: 58.2232 Evaluate side-chains 270 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 203 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 ASN D 179 ASN D 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8244 Z= 0.158 Angle : 0.684 12.339 11112 Z= 0.334 Chirality : 0.042 0.180 1260 Planarity : 0.004 0.032 1272 Dihedral : 17.509 102.910 1552 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 8.33 % Allowed : 34.31 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 896 helix: 0.51 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 54 HIS 0.001 0.000 HIS D 52 PHE 0.017 0.001 PHE A 94 TYR 0.006 0.001 TYR E 49 ARG 0.001 0.000 ARG E 202 *********************** 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 274 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 206 time to evaluate : 1.114 Fit side-chains REVERT: A 54 TRP cc_start: 0.7670 (p90) cc_final: 0.7191 (p-90) REVERT: A 63 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9177 (mm) REVERT: A 81 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8425 (mmmt) REVERT: A 101 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9085 (mm) REVERT: C 43 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: C 63 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9122 (mm) REVERT: C 81 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8360 (mmmt) REVERT: C 147 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8712 (pp) REVERT: C 202 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8942 (mmt90) REVERT: D 63 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9152 (mm) REVERT: D 81 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8364 (mmmt) REVERT: D 101 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9135 (mm) REVERT: D 202 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8942 (mmt90) REVERT: D 208 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8032 (m) REVERT: E 54 TRP cc_start: 0.7681 (p90) cc_final: 0.7293 (p-90) REVERT: E 60 ASP cc_start: 0.8709 (t70) cc_final: 0.8089 (t0) REVERT: E 63 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8990 (mt) REVERT: E 81 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8432 (mmmt) REVERT: E 207 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7448 (mm-30) outliers start: 68 outliers final: 51 residues processed: 253 average time/residue: 0.1800 time to fit residues: 63.2555 Evaluate side-chains 267 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8244 Z= 0.185 Angle : 0.690 12.148 11112 Z= 0.340 Chirality : 0.043 0.182 1260 Planarity : 0.004 0.031 1272 Dihedral : 17.427 105.382 1550 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 8.33 % Allowed : 34.31 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 896 helix: 0.55 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 54 HIS 0.001 0.000 HIS C 22 PHE 0.016 0.001 PHE D 94 TYR 0.005 0.001 TYR C 49 ARG 0.002 0.000 ARG A 202 ********************** 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 275 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 207 time to evaluate : 0.937 Fit side-chains REVERT: A 54 TRP cc_start: 0.7811 (p90) cc_final: 0.7305 (p-90) REVERT: A 63 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9182 (mm) REVERT: A 81 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8440 (mmmt) REVERT: A 101 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9049 (mm) REVERT: C 40 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8729 (p) REVERT: C 43 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: C 54 TRP cc_start: 0.7610 (p90) cc_final: 0.7316 (p-90) REVERT: C 63 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9134 (mm) REVERT: C 81 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8349 (mmmt) REVERT: C 106 LEU cc_start: 0.8880 (tp) cc_final: 0.8646 (tt) REVERT: C 147 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8708 (pp) REVERT: C 202 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8946 (mmt90) REVERT: D 54 TRP cc_start: 0.7632 (p90) cc_final: 0.7288 (p-90) REVERT: D 60 ASP cc_start: 0.8733 (t70) cc_final: 0.8138 (t0) REVERT: D 63 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9153 (mm) REVERT: D 81 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8361 (mmmt) REVERT: D 101 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9110 (mm) REVERT: D 202 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8961 (mmt90) REVERT: E 54 TRP cc_start: 0.7750 (p90) cc_final: 0.7288 (p-90) REVERT: E 63 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8839 (mt) REVERT: E 81 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8436 (mmmt) REVERT: E 207 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7465 (mm-30) outliers start: 68 outliers final: 55 residues processed: 255 average time/residue: 0.1589 time to fit residues: 57.5968 Evaluate side-chains 268 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 202 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097734 restraints weight = 15227.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101007 restraints weight = 6680.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103113 restraints weight = 4131.003| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3894 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= 0.171 Angle : 0.689 12.044 11112 Z= 0.340 Chirality : 0.042 0.174 1260 Planarity : 0.004 0.031 1272 Dihedral : 17.122 104.350 1550 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 7.84 % Allowed : 35.29 % Favored : 56.86 % 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 (0.29), residues: 896 helix: 0.38 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 54 HIS 0.001 0.000 HIS A 22 PHE 0.016 0.001 PHE A 94 TYR 0.006 0.001 TYR E 49 ARG 0.002 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.04 seconds wall clock time: 34 minutes 20.78 seconds (2060.78 seconds total)