Starting phenix.real_space_refine on Mon Nov 17 20:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_21446.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_21446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_21446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_21446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxo_21446/11_2025/6vxo_21446.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 6 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: "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} Restraints were copied for chains: E Time building chain proxies: 2.29, per 1000 atoms: 0.28 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 - 3.00 Amino acid : True - 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: 0.64 Conformation dependent library (CDL) restraints added in 382.7 milliseconds 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... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 4.283A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE A 56 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 148 through 169 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 187 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE C 56 " --> pdb=" O HIS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 122' Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 148 through 169 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 187 Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 235 removed outlier: 3.960A pdb=" N PHE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE D 56 " --> pdb=" O HIS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 122' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 130 through 143 Processing helix chain 'D' and resid 148 through 169 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 187 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 43 removed outlier: 4.285A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE E 56 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 106 removed outlier: 3.546A pdb=" N TRP E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.892A pdb=" N LEU E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 122' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 148 through 169 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 187 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1284 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: 1.08 Time building geometry restraints manager: 0.86 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: 0.00 - 2.32: 10386 2.32 - 4.65: 483 4.65 - 6.97: 163 6.97 - 9.30: 48 9.30 - 11.62: 32 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: 307 2.68 - 3.24: 8646 3.24 - 3.79: 12731 3.79 - 4.35: 15410 4.35 - 4.90: 25309 Nonbonded interactions: 62403 Sorted by model distance: nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR E 214 " pdb=" OG SER E 217 " model vdw 2.126 3.040 nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 217 " model vdw 2.126 3.040 nonbonded pdb=" O PHE E 161 " pdb=" OH TYR E 214 " model vdw 2.219 3.040 ... (remaining 62398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 302) selection = chain 'C' selection = (chain 'D' and resid 15 through 302) selection = (chain 'E' and resid 15 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- 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= 0.586 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG E 122 TYR 0.007 0.001 TYR A 159 PHE 0.017 0.002 PHE C 205 TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.01229 ( 8244) covalent geometry : angle 1.40070 (11112) hydrogen bonds : bond 0.17884 ( 428) hydrogen bonds : angle 7.61056 ( 1284) *********************** 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 to be fit. rotamer outliers: 176 poor density : 207 time to evaluate : 0.274 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: 0.0662 time to fit residues: 33.0959 Evaluate side-chains 329 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 180 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 90 ASN A 170 GLN A 181 GLN A 237 ASN C 90 ASN C 170 GLN C 181 GLN C 237 ASN D 90 ASN D 170 GLN D 181 GLN D 237 ASN E 90 ASN E 170 GLN E 181 GLN E 237 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095578 restraints weight = 16094.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098732 restraints weight = 7162.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100801 restraints weight = 4402.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101993 restraints weight = 3300.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102740 restraints weight = 2807.238| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8244 Z= 0.144 Angle : 0.622 5.904 11112 Z= 0.321 Chirality : 0.041 0.154 1260 Planarity : 0.003 0.019 1272 Dihedral : 23.639 109.875 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 9.80 % Allowed : 23.53 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.28), residues: 896 helix: 0.26 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.89 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.011 0.001 TYR D 214 PHE 0.014 0.001 PHE A 205 TRP 0.011 0.001 TRP E 65 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8244) covalent geometry : angle 0.62219 (11112) hydrogen bonds : bond 0.04363 ( 428) hydrogen bonds : angle 4.29322 ( 1284) *********************** 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 301 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8323 (m-80) cc_final: 0.7978 (m-80) REVERT: A 53 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8171 (tptp) REVERT: A 65 TRP cc_start: 0.8063 (m100) cc_final: 0.7707 (t-100) REVERT: A 207 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 45 TYR cc_start: 0.8332 (m-80) cc_final: 0.7986 (m-80) REVERT: C 53 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8209 (tptp) REVERT: C 54 TRP cc_start: 0.7002 (p-90) cc_final: 0.6800 (p-90) REVERT: C 65 TRP cc_start: 0.8053 (m100) cc_final: 0.7702 (t-100) REVERT: C 207 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 45 TYR cc_start: 0.8361 (m-80) cc_final: 0.8016 (m-80) REVERT: D 53 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8147 (tptp) REVERT: D 65 TRP cc_start: 0.8051 (m100) cc_final: 0.7689 (t-100) REVERT: D 207 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7552 (mm-30) REVERT: E 45 TYR cc_start: 0.8350 (m-80) cc_final: 0.8031 (m-80) REVERT: E 65 TRP cc_start: 0.8093 (m100) cc_final: 0.7729 (t-100) REVERT: E 207 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7587 (mm-30) outliers start: 80 outliers final: 40 residues processed: 288 average time/residue: 0.0620 time to fit residues: 27.3659 Evaluate side-chains 252 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 SER 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 149 ASN Chi-restraints excluded: chain A residue 179 ASN 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 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER 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 149 ASN 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 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER 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 149 ASN 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 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 100 SER 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 149 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU 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 22 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN C 228 ASN D 228 ASN E 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099835 restraints weight = 15642.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103051 restraints weight = 6952.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105140 restraints weight = 4257.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106287 restraints weight = 3184.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107175 restraints weight = 2708.138| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2827 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= 0.112 Angle : 0.612 7.577 11112 Z= 0.307 Chirality : 0.043 0.172 1260 Planarity : 0.003 0.019 1272 Dihedral : 21.607 107.074 1549 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 10.05 % Allowed : 26.59 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.30), residues: 896 helix: 0.63 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -2.05 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 202 TYR 0.004 0.001 TYR C 214 PHE 0.026 0.001 PHE C 94 TRP 0.009 0.001 TRP E 65 HIS 0.001 0.000 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8244) covalent geometry : angle 0.61180 (11112) hydrogen bonds : bond 0.03836 ( 428) hydrogen bonds : angle 3.83515 ( 1284) *********************** 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 326 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 244 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8154 (m-80) cc_final: 0.7751 (m-80) REVERT: A 65 TRP cc_start: 0.7936 (m100) cc_final: 0.7619 (t-100) REVERT: A 158 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.9075 (m-80) REVERT: A 202 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8775 (tpp-160) REVERT: C 45 TYR cc_start: 0.8184 (m-80) cc_final: 0.7757 (m-80) REVERT: C 63 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9140 (mm) REVERT: C 65 TRP cc_start: 0.7969 (m100) cc_final: 0.7580 (t-100) REVERT: C 73 MET cc_start: 0.6413 (tpt) cc_final: 0.6147 (tpt) REVERT: C 138 ASP cc_start: 0.8237 (t0) cc_final: 0.8030 (t0) REVERT: C 158 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9131 (m-80) REVERT: C 202 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (tpp-160) REVERT: D 63 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9183 (mm) REVERT: D 65 TRP cc_start: 0.7980 (m100) cc_final: 0.7601 (t-100) REVERT: D 138 ASP cc_start: 0.8217 (t0) cc_final: 0.8005 (t0) REVERT: D 158 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9129 (m-80) REVERT: D 207 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7567 (mm-30) REVERT: E 45 TYR cc_start: 0.8141 (m-80) cc_final: 0.7733 (m-80) REVERT: E 65 TRP cc_start: 0.8061 (m100) cc_final: 0.7634 (t-100) REVERT: E 138 ASP cc_start: 0.8208 (t0) cc_final: 0.8004 (t0) REVERT: E 158 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9079 (m-80) REVERT: E 202 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (tpp-160) outliers start: 82 outliers final: 44 residues processed: 311 average time/residue: 0.0669 time to fit residues: 30.7925 Evaluate side-chains 252 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 100 SER 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 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER 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 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 187 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 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER 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 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 71 ILE 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 149 ASN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU 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 31 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095701 restraints weight = 15791.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098921 restraints weight = 7123.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101082 restraints weight = 4418.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102294 restraints weight = 3341.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103174 restraints weight = 2864.185| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8244 Z= 0.141 Angle : 0.685 13.009 11112 Z= 0.330 Chirality : 0.043 0.158 1260 Planarity : 0.003 0.024 1272 Dihedral : 20.962 105.813 1536 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 10.91 % Allowed : 25.74 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.29), residues: 896 helix: 0.89 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.21 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.013 0.001 TYR A 214 PHE 0.031 0.001 PHE E 94 TRP 0.010 0.001 TRP C 65 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8244) covalent geometry : angle 0.68486 (11112) hydrogen bonds : bond 0.04027 ( 428) hydrogen bonds : angle 3.84845 ( 1284) *********************** 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 293 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8213 (m-80) cc_final: 0.7754 (m-80) REVERT: A 63 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9098 (mm) REVERT: A 65 TRP cc_start: 0.7989 (m100) cc_final: 0.7785 (t-100) REVERT: A 73 MET cc_start: 0.6538 (tpt) cc_final: 0.6309 (tpt) REVERT: A 158 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: C 45 TYR cc_start: 0.8207 (m-80) cc_final: 0.7749 (m-80) REVERT: C 63 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9225 (mm) REVERT: C 65 TRP cc_start: 0.8037 (m100) cc_final: 0.7813 (t-100) REVERT: C 73 MET cc_start: 0.6374 (tpt) cc_final: 0.6118 (tpt) REVERT: C 138 ASP cc_start: 0.8267 (t0) cc_final: 0.8053 (t0) REVERT: C 158 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9146 (m-80) REVERT: D 54 TRP cc_start: 0.6995 (p-90) cc_final: 0.6782 (p-90) REVERT: D 65 TRP cc_start: 0.7982 (m100) cc_final: 0.7620 (t-100) REVERT: D 158 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9123 (m-80) REVERT: D 207 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7567 (mm-30) REVERT: E 45 TYR cc_start: 0.8262 (m-80) cc_final: 0.7807 (m-80) REVERT: E 53 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8299 (tptp) REVERT: E 63 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9098 (mm) REVERT: E 158 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9094 (m-80) outliers start: 89 outliers final: 66 residues processed: 272 average time/residue: 0.0610 time to fit residues: 25.7122 Evaluate side-chains 275 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 202 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER 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 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 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 55 LEU 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 100 SER 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 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 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 55 LEU 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 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 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 55 LEU 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 109 VAL Chi-restraints excluded: chain E residue 127 ILE 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 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.122747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097289 restraints weight = 15570.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100496 restraints weight = 6946.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102619 restraints weight = 4309.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103796 restraints weight = 3262.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104657 restraints weight = 2808.211| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8244 Z= 0.125 Angle : 0.680 12.601 11112 Z= 0.323 Chirality : 0.043 0.163 1260 Planarity : 0.003 0.026 1272 Dihedral : 19.981 105.748 1532 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 10.05 % Allowed : 28.55 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.29), residues: 896 helix: 0.72 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.81 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 202 TYR 0.010 0.001 TYR C 214 PHE 0.026 0.001 PHE E 94 TRP 0.010 0.001 TRP D 65 HIS 0.001 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8244) covalent geometry : angle 0.68019 (11112) hydrogen bonds : bond 0.03895 ( 428) hydrogen bonds : angle 3.67387 ( 1284) *********************** 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 307 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 225 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: A 45 TYR cc_start: 0.8147 (m-80) cc_final: 0.7681 (m-80) REVERT: A 54 TRP cc_start: 0.7020 (p-90) cc_final: 0.6784 (p-90) REVERT: A 63 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9108 (mm) REVERT: A 158 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9104 (m-80) REVERT: C 45 TYR cc_start: 0.8149 (m-80) cc_final: 0.7673 (m-80) REVERT: C 54 TRP cc_start: 0.7031 (p-90) cc_final: 0.6784 (p-90) REVERT: C 63 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8978 (mt) REVERT: C 73 MET cc_start: 0.6136 (tpt) cc_final: 0.5899 (tpt) REVERT: C 158 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9136 (m-80) REVERT: C 220 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8714 (mm) REVERT: D 45 TYR cc_start: 0.8207 (m-80) cc_final: 0.7814 (m-80) REVERT: D 54 TRP cc_start: 0.7011 (p-90) cc_final: 0.6768 (p-90) REVERT: D 158 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9162 (m-80) REVERT: E 45 TYR cc_start: 0.8216 (m-80) cc_final: 0.7741 (m-80) REVERT: E 63 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9107 (mm) REVERT: E 154 MET cc_start: 0.8414 (tpt) cc_final: 0.8162 (tpt) REVERT: E 158 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9149 (m-80) REVERT: E 220 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8666 (mm) outliers start: 82 outliers final: 61 residues processed: 288 average time/residue: 0.0617 time to fit residues: 26.9216 Evaluate side-chains 282 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU 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 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 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 40 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 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 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 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE 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 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 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 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099473 restraints weight = 15524.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102690 restraints weight = 6826.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104820 restraints weight = 4177.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106106 restraints weight = 3135.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106706 restraints weight = 2657.615| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8244 Z= 0.127 Angle : 0.734 13.139 11112 Z= 0.343 Chirality : 0.043 0.171 1260 Planarity : 0.003 0.040 1272 Dihedral : 18.977 105.242 1527 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 10.54 % Allowed : 29.66 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 896 helix: 0.92 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 119 TYR 0.012 0.001 TYR E 214 PHE 0.024 0.001 PHE E 94 TRP 0.011 0.001 TRP E 196 HIS 0.001 0.000 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8244) covalent geometry : angle 0.73439 (11112) hydrogen bonds : bond 0.03872 ( 428) hydrogen bonds : angle 3.62871 ( 1284) *********************** 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 308 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: A 45 TYR cc_start: 0.8112 (m-80) cc_final: 0.7616 (m-80) REVERT: A 54 TRP cc_start: 0.6970 (p-90) cc_final: 0.6740 (p-90) REVERT: A 63 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9031 (mm) REVERT: A 158 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.9074 (m-80) REVERT: C 43 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: C 45 TYR cc_start: 0.8161 (m-80) cc_final: 0.7646 (m-80) REVERT: C 54 TRP cc_start: 0.6977 (p-90) cc_final: 0.6770 (p-90) REVERT: C 63 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9002 (mt) REVERT: C 158 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9100 (m-80) REVERT: D 45 TYR cc_start: 0.8206 (m-80) cc_final: 0.7825 (m-80) REVERT: D 54 TRP cc_start: 0.6988 (p-90) cc_final: 0.6754 (p-90) REVERT: D 63 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9157 (mm) REVERT: D 154 MET cc_start: 0.8363 (tpt) cc_final: 0.8137 (tpt) REVERT: D 158 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.9090 (m-80) REVERT: E 40 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8895 (p) REVERT: E 43 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: E 45 TYR cc_start: 0.8109 (m-80) cc_final: 0.7606 (m-80) REVERT: E 54 TRP cc_start: 0.6998 (p-90) cc_final: 0.6774 (p-90) REVERT: E 63 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8997 (mm) REVERT: E 154 MET cc_start: 0.8348 (tpt) cc_final: 0.8109 (tpt) REVERT: E 158 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9110 (m-80) outliers start: 86 outliers final: 64 residues processed: 283 average time/residue: 0.0656 time to fit residues: 27.8819 Evaluate side-chains 284 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 43 GLU 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 100 SER 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 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 187 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 40 VAL 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 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 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 85 PHE 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 104 LEU Chi-restraints excluded: chain D residue 127 ILE 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 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU 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 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE 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 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.0770 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100116 restraints weight = 15658.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103411 restraints weight = 6908.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105572 restraints weight = 4238.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106776 restraints weight = 3181.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107598 restraints weight = 2716.614| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8244 Z= 0.123 Angle : 0.724 13.164 11112 Z= 0.340 Chirality : 0.043 0.173 1260 Planarity : 0.003 0.040 1272 Dihedral : 18.095 104.160 1526 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 9.44 % Allowed : 31.13 % Favored : 59.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.28), residues: 896 helix: 0.76 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.97 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 202 TYR 0.010 0.001 TYR D 214 PHE 0.021 0.001 PHE E 94 TRP 0.005 0.001 TRP A 196 HIS 0.001 0.000 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8244) covalent geometry : angle 0.72428 (11112) hydrogen bonds : bond 0.03784 ( 428) hydrogen bonds : angle 3.69934 ( 1284) *********************** 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 293 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 216 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8706 (p) REVERT: A 43 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7686 (pp20) REVERT: A 54 TRP cc_start: 0.6933 (p-90) cc_final: 0.6703 (p-90) REVERT: A 63 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8935 (mm) REVERT: A 158 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.9047 (m-80) REVERT: A 201 MET cc_start: 0.8504 (ttp) cc_final: 0.8271 (ttm) REVERT: A 220 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 40 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 43 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7666 (pp20) REVERT: C 158 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.9090 (m-80) REVERT: C 220 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8619 (mt) REVERT: D 45 TYR cc_start: 0.8140 (m-80) cc_final: 0.7779 (m-80) REVERT: D 63 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9101 (mm) REVERT: D 158 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9131 (m-80) REVERT: D 220 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8691 (mt) REVERT: E 40 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8889 (p) REVERT: E 43 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: E 54 TRP cc_start: 0.6974 (p-90) cc_final: 0.6729 (p-90) REVERT: E 63 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8928 (mm) REVERT: E 154 MET cc_start: 0.8318 (tpt) cc_final: 0.8077 (tpt) REVERT: E 158 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9080 (m-80) REVERT: E 220 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 77 outliers final: 53 residues processed: 267 average time/residue: 0.0653 time to fit residues: 26.2156 Evaluate side-chains 274 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 204 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 43 GLU 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 100 SER 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 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 187 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 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 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 85 PHE 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 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU 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 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 85 PHE 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 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 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 59 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095898 restraints weight = 15744.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099108 restraints weight = 7049.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101203 restraints weight = 4371.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102378 restraints weight = 3311.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103217 restraints weight = 2843.407| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8244 Z= 0.174 Angle : 0.752 13.456 11112 Z= 0.362 Chirality : 0.045 0.172 1260 Planarity : 0.003 0.034 1272 Dihedral : 18.333 110.063 1520 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 9.44 % Allowed : 31.62 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 896 helix: 0.93 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 58 TYR 0.027 0.002 TYR D 159 PHE 0.019 0.001 PHE E 94 TRP 0.007 0.001 TRP A 212 HIS 0.002 0.001 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8244) covalent geometry : angle 0.75192 (11112) hydrogen bonds : bond 0.04025 ( 428) hydrogen bonds : angle 3.83142 ( 1284) *********************** 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 285 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 208 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 43 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: A 45 TYR cc_start: 0.8118 (m-80) cc_final: 0.7612 (m-80) REVERT: A 54 TRP cc_start: 0.7091 (p-90) cc_final: 0.6819 (p-90) REVERT: A 63 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9008 (mm) REVERT: A 201 MET cc_start: 0.8584 (ttp) cc_final: 0.8357 (ttm) REVERT: A 220 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8627 (mm) REVERT: C 40 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8778 (p) REVERT: C 43 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7692 (pp20) REVERT: C 45 TYR cc_start: 0.8109 (m-80) cc_final: 0.7595 (m-80) REVERT: C 73 MET cc_start: 0.6480 (tpt) cc_final: 0.6250 (tpt) REVERT: C 158 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9108 (m-80) REVERT: C 220 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8642 (mm) REVERT: D 45 TYR cc_start: 0.8214 (m-80) cc_final: 0.7840 (m-80) REVERT: D 63 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9083 (mm) REVERT: D 158 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9172 (m-80) REVERT: D 220 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 40 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8849 (p) REVERT: E 43 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: E 45 TYR cc_start: 0.8097 (m-80) cc_final: 0.7551 (m-80) REVERT: E 54 TRP cc_start: 0.6998 (p-90) cc_final: 0.6748 (p-90) REVERT: E 63 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8998 (mm) REVERT: E 154 MET cc_start: 0.8412 (tpt) cc_final: 0.8194 (tpt) REVERT: E 158 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9119 (m-80) REVERT: E 220 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8659 (mm) outliers start: 77 outliers final: 58 residues processed: 263 average time/residue: 0.0655 time to fit residues: 25.7706 Evaluate side-chains 278 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 204 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 43 GLU 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 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 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 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 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 85 PHE 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 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU 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 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 85 PHE 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 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 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: 0.7980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.123034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098200 restraints weight = 15727.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101447 restraints weight = 7091.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103569 restraints weight = 4404.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104869 restraints weight = 3329.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105513 restraints weight = 2834.891| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8244 Z= 0.133 Angle : 0.726 13.053 11112 Z= 0.349 Chirality : 0.045 0.185 1260 Planarity : 0.003 0.031 1272 Dihedral : 17.757 108.347 1520 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 9.07 % Allowed : 32.60 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 896 helix: 0.78 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 202 TYR 0.009 0.001 TYR A 214 PHE 0.020 0.001 PHE E 94 TRP 0.006 0.001 TRP A 212 HIS 0.001 0.000 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8244) covalent geometry : angle 0.72629 (11112) hydrogen bonds : bond 0.03832 ( 428) hydrogen bonds : angle 3.74312 ( 1284) *********************** 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 273 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: A 54 TRP cc_start: 0.6988 (p-90) cc_final: 0.6745 (p-90) REVERT: A 63 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 220 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 40 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8728 (p) REVERT: C 43 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: C 45 TYR cc_start: 0.8077 (m-80) cc_final: 0.7566 (m-80) REVERT: C 73 MET cc_start: 0.6409 (tpt) cc_final: 0.6185 (tpt) REVERT: C 158 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: C 220 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8472 (mt) REVERT: D 45 TYR cc_start: 0.8217 (m-80) cc_final: 0.7889 (m-80) REVERT: D 63 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9026 (mm) REVERT: D 158 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9119 (m-80) REVERT: D 159 TYR cc_start: 0.8642 (t80) cc_final: 0.8330 (t80) REVERT: D 220 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8607 (mt) REVERT: E 40 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8921 (p) REVERT: E 43 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7621 (pp20) REVERT: E 45 TYR cc_start: 0.8116 (m-80) cc_final: 0.7613 (m-80) REVERT: E 54 TRP cc_start: 0.6907 (p-90) cc_final: 0.6669 (p-90) REVERT: E 63 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8935 (mm) REVERT: E 154 MET cc_start: 0.8364 (tpt) cc_final: 0.8142 (tpt) REVERT: E 158 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9100 (m-80) REVERT: E 220 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8552 (mt) outliers start: 74 outliers final: 54 residues processed: 249 average time/residue: 0.0674 time to fit residues: 25.0773 Evaluate side-chains 265 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 43 GLU 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 143 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 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 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU 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 63 LEU Chi-restraints excluded: chain D residue 85 PHE 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 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 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 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE 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 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 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 24 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 0.0000 chunk 55 optimal weight: 0.0570 overall best weight: 0.3280 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102261 restraints weight = 15263.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105499 restraints weight = 6956.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107679 restraints weight = 4344.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109051 restraints weight = 3281.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109470 restraints weight = 2782.594| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8244 Z= 0.117 Angle : 0.720 12.811 11112 Z= 0.342 Chirality : 0.043 0.179 1260 Planarity : 0.003 0.030 1272 Dihedral : 16.643 101.828 1516 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 7.97 % Allowed : 33.82 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 896 helix: 0.83 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.36 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.010 0.001 TYR C 159 PHE 0.019 0.001 PHE E 94 TRP 0.006 0.001 TRP A 196 HIS 0.002 0.000 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8244) covalent geometry : angle 0.72019 (11112) hydrogen bonds : bond 0.03538 ( 428) hydrogen bonds : angle 3.63231 ( 1284) ********************** 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 282 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8721 (p) REVERT: A 43 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: A 63 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 81 LYS cc_start: 0.8783 (tptm) cc_final: 0.8405 (mmmt) REVERT: A 159 TYR cc_start: 0.8381 (t80) cc_final: 0.8160 (t80) REVERT: A 201 MET cc_start: 0.8461 (ttp) cc_final: 0.8182 (ttp) REVERT: A 220 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 40 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8556 (p) REVERT: C 43 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7678 (pp20) REVERT: C 63 LEU cc_start: 0.9054 (mm) cc_final: 0.8847 (mm) REVERT: C 73 MET cc_start: 0.6476 (tpt) cc_final: 0.6247 (tpt) REVERT: C 81 LYS cc_start: 0.8750 (tptm) cc_final: 0.8394 (mmmt) REVERT: C 158 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.9072 (m-80) REVERT: C 220 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 45 TYR cc_start: 0.8186 (m-80) cc_final: 0.7880 (m-80) REVERT: D 54 TRP cc_start: 0.6941 (p-90) cc_final: 0.6682 (p-90) REVERT: D 63 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8895 (mm) REVERT: D 81 LYS cc_start: 0.8864 (tptm) cc_final: 0.8452 (mmmt) REVERT: D 158 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9112 (m-80) REVERT: D 220 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8412 (mt) REVERT: E 40 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8754 (p) REVERT: E 43 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7640 (pp20) REVERT: E 54 TRP cc_start: 0.6924 (p-90) cc_final: 0.6661 (p-90) REVERT: E 63 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8857 (mm) REVERT: E 81 LYS cc_start: 0.8874 (tptm) cc_final: 0.8459 (mmmt) REVERT: E 158 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9103 (m-80) REVERT: E 220 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8363 (mt) outliers start: 65 outliers final: 40 residues processed: 266 average time/residue: 0.0651 time to fit residues: 25.9221 Evaluate side-chains 260 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU 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 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU 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 63 LEU Chi-restraints excluded: chain D residue 85 PHE 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 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 187 LEU 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 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE 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 127 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099218 restraints weight = 15646.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102578 restraints weight = 6920.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104734 restraints weight = 4262.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106070 restraints weight = 3205.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106764 restraints weight = 2723.959| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8244 Z= 0.131 Angle : 0.733 13.516 11112 Z= 0.353 Chirality : 0.044 0.175 1260 Planarity : 0.003 0.029 1272 Dihedral : 16.592 99.607 1516 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 7.35 % Allowed : 36.15 % Favored : 56.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 896 helix: 0.66 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.88 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.012 0.001 TYR E 214 PHE 0.018 0.001 PHE E 94 TRP 0.006 0.000 TRP A 212 HIS 0.001 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8244) covalent geometry : angle 0.73296 (11112) hydrogen bonds : bond 0.03724 ( 428) hydrogen bonds : angle 3.68794 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.49 seconds wall clock time: 25 minutes 39.13 seconds (1539.13 seconds total)