Starting phenix.real_space_refine on Wed Feb 12 20:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxo_21446/02_2025/6vxo_21446.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxo_21446/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/02_2025/6vxo_21446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxo_21446/02_2025/6vxo_21446.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxo_21446/02_2025/6vxo_21446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxo_21446/02_2025/6vxo_21446.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 24 5.16 5 C 5548 2.51 5 N 1184 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.66, per 1000 atoms: 0.70 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... 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: 0.71 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: 1.98 Time building geometry restraints manager: 2.54 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 240 or resid 301 through 302)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 240 or resid 301 through 302)) selection = (chain 'E' and (resid 15 through 240 or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.620 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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= 0.771 Angle : 1.401 11.619 11112 Z= 0.585 Chirality : 0.047 0.132 1260 Planarity : 0.005 0.035 1272 Dihedral : 24.970 120.396 3156 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.17 % Favored : 87.39 % Rotamer: Outliers : 21.57 % Allowed : 21.08 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.24), residues: 896 helix: -1.88 (0.17), residues: 640 sheet: None (None), residues: 0 loop : -4.16 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 PHE 0.017 0.002 PHE C 205 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 207 time to evaluate : 1.385 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: 0.1516 time to fit residues: 73.6105 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 : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 170 GLN A 181 GLN A 189 GLN A 237 ASN C 90 ASN C 170 GLN C 181 GLN C 189 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.120491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095741 restraints weight = 15842.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098861 restraints weight = 7093.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100927 restraints weight = 4395.712| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8244 Z= 0.198 Angle : 0.622 6.048 11112 Z= 0.319 Chirality : 0.041 0.155 1260 Planarity : 0.003 0.020 1272 Dihedral : 23.708 109.764 1756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 9.68 % Allowed : 23.53 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.29), residues: 896 helix: 0.27 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.001 0.001 HIS C 52 PHE 0.014 0.001 PHE D 205 TYR 0.012 0.002 TYR D 214 ARG 0.001 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 220 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8362 (m-80) cc_final: 0.8015 (m-80) REVERT: A 53 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8137 (tptp) REVERT: A 65 TRP cc_start: 0.8109 (m100) cc_final: 0.7740 (t-100) REVERT: A 207 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 45 TYR cc_start: 0.8370 (m-80) cc_final: 0.8013 (m-80) REVERT: C 54 TRP cc_start: 0.7024 (p-90) cc_final: 0.6817 (p-90) REVERT: C 65 TRP cc_start: 0.8073 (m100) cc_final: 0.7712 (t-100) REVERT: C 207 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7595 (mm-30) REVERT: C 231 ILE cc_start: 0.8591 (mt) cc_final: 0.8389 (mt) REVERT: D 45 TYR cc_start: 0.8370 (m-80) cc_final: 0.7992 (m-80) REVERT: D 49 TYR cc_start: 0.8320 (t80) cc_final: 0.8118 (t80) REVERT: D 53 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8136 (tptp) REVERT: D 65 TRP cc_start: 0.8070 (m100) cc_final: 0.7698 (t-100) REVERT: D 138 ASP cc_start: 0.8291 (t0) cc_final: 0.8050 (t0) REVERT: D 207 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 45 TYR cc_start: 0.8411 (m-80) cc_final: 0.8084 (m-80) REVERT: E 65 TRP cc_start: 0.8147 (m100) cc_final: 0.7767 (t-100) REVERT: E 202 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8751 (tpp-160) REVERT: E 207 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7586 (mm-30) outliers start: 79 outliers final: 38 residues processed: 287 average time/residue: 0.1493 time to fit residues: 62.5746 Evaluate side-chains 252 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 189 GLN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN 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 = 0.3761 r_free = 0.3761 target = 0.121917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097283 restraints weight = 15950.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100486 restraints weight = 7150.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102569 restraints weight = 4414.707| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8244 Z= 0.173 Angle : 0.617 7.605 11112 Z= 0.312 Chirality : 0.043 0.165 1260 Planarity : 0.003 0.018 1272 Dihedral : 21.879 108.829 1546 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 10.17 % Allowed : 25.49 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.30), residues: 896 helix: 0.77 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.16 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.001 0.000 HIS C 22 PHE 0.026 0.001 PHE C 94 TYR 0.004 0.001 TYR E 214 ARG 0.001 0.000 ARG E 116 *********************** 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 322 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 239 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8212 (m-80) cc_final: 0.7806 (m-80) REVERT: A 63 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9193 (mm) REVERT: A 65 TRP cc_start: 0.7914 (m100) cc_final: 0.7567 (t-100) REVERT: A 73 MET cc_start: 0.6487 (tpt) cc_final: 0.6261 (tpt) REVERT: A 158 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9092 (m-80) REVERT: A 202 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8787 (tpp-160) REVERT: A 207 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 45 TYR cc_start: 0.8218 (m-80) cc_final: 0.7802 (m-80) REVERT: C 65 TRP cc_start: 0.7912 (m100) cc_final: 0.7684 (t-100) REVERT: C 73 MET cc_start: 0.6665 (tpt) cc_final: 0.6394 (tpt) REVERT: C 138 ASP cc_start: 0.8253 (t0) cc_final: 0.8046 (t0) REVERT: C 158 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9178 (m-80) REVERT: C 207 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 45 TYR cc_start: 0.8157 (m-80) cc_final: 0.7762 (m-80) REVERT: D 63 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9166 (mm) REVERT: D 65 TRP cc_start: 0.8017 (m100) cc_final: 0.7739 (t-100) REVERT: D 158 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9151 (m-80) REVERT: D 202 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8859 (tpp-160) REVERT: D 207 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7507 (mm-30) REVERT: E 45 TYR cc_start: 0.8250 (m-80) cc_final: 0.7844 (m-80) REVERT: E 63 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9184 (mm) REVERT: E 65 TRP cc_start: 0.8022 (m100) cc_final: 0.7761 (t-100) REVERT: E 138 ASP cc_start: 0.8237 (t0) cc_final: 0.8029 (t0) REVERT: E 158 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9097 (m-80) REVERT: E 201 MET cc_start: 0.8497 (ttt) cc_final: 0.8205 (ttp) REVERT: E 207 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 83 outliers final: 51 residues processed: 307 average time/residue: 0.1453 time to fit residues: 65.0566 Evaluate side-chains 264 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 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 179 ASN 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 228 ASN 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 179 ASN 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 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 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 202 ARG 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 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 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 189 GLN 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 2 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096659 restraints weight = 15664.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099894 restraints weight = 7028.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101982 restraints weight = 4371.120| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8244 Z= 0.200 Angle : 0.657 12.526 11112 Z= 0.322 Chirality : 0.043 0.161 1260 Planarity : 0.003 0.024 1272 Dihedral : 21.096 106.030 1543 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 10.78 % Allowed : 25.61 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 896 helix: 0.90 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.13 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 54 HIS 0.002 0.001 HIS A 52 PHE 0.029 0.001 PHE D 94 TYR 0.010 0.001 TYR A 214 ARG 0.001 0.000 ARG A 58 *********************** 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 299 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 211 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8186 (m-80) cc_final: 0.7734 (m-80) REVERT: A 63 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9126 (mm) REVERT: A 65 TRP cc_start: 0.8071 (m100) cc_final: 0.7844 (t-100) REVERT: A 158 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9087 (m-80) REVERT: A 202 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (tpp-160) REVERT: C 45 TYR cc_start: 0.8184 (m-80) cc_final: 0.7708 (m-80) REVERT: C 53 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8331 (tptp) REVERT: C 63 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9111 (mm) REVERT: C 65 TRP cc_start: 0.8079 (m100) cc_final: 0.7704 (t-100) REVERT: C 73 MET cc_start: 0.6347 (tpt) cc_final: 0.6100 (tpt) REVERT: C 138 ASP cc_start: 0.8289 (t0) cc_final: 0.8079 (t0) REVERT: C 158 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9127 (m-80) REVERT: D 53 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8204 (tptp) REVERT: D 55 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8394 (pt) REVERT: D 63 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 65 TRP cc_start: 0.8094 (m100) cc_final: 0.7672 (t-100) REVERT: D 158 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9167 (m-80) REVERT: D 202 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8818 (tpp-160) REVERT: D 207 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7578 (mm-30) REVERT: E 45 TYR cc_start: 0.8267 (m-80) cc_final: 0.7802 (m-80) REVERT: E 53 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8202 (tptp) REVERT: E 65 TRP cc_start: 0.8064 (m100) cc_final: 0.7698 (t-100) REVERT: E 158 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9109 (m-80) REVERT: E 207 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7595 (mm-30) outliers start: 88 outliers final: 64 residues processed: 277 average time/residue: 0.1487 time to fit residues: 60.0200 Evaluate side-chains 281 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 207 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 202 ARG 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 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 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 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 51 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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** A 228 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.123580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098134 restraints weight = 15323.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101413 restraints weight = 6849.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103582 restraints weight = 4243.754| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8244 Z= 0.172 Angle : 0.681 12.764 11112 Z= 0.322 Chirality : 0.043 0.165 1260 Planarity : 0.003 0.026 1272 Dihedral : 20.002 105.809 1534 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 9.93 % Allowed : 28.31 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.29), residues: 896 helix: 0.72 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.001 0.000 HIS C 22 PHE 0.024 0.001 PHE D 94 TYR 0.011 0.001 TYR A 214 ARG 0.001 0.000 ARG D 202 *********************** 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 305 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 224 time to evaluate : 0.862 Fit side-chains REVERT: A 43 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7652 (pp20) REVERT: A 45 TYR cc_start: 0.8195 (m-80) cc_final: 0.7726 (m-80) REVERT: A 63 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8957 (mt) REVERT: A 158 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9185 (m-80) REVERT: C 43 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: C 45 TYR cc_start: 0.8168 (m-80) cc_final: 0.7652 (m-80) REVERT: C 53 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8302 (tptp) REVERT: C 63 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9141 (mm) REVERT: C 73 MET cc_start: 0.6171 (tpt) cc_final: 0.5920 (tpt) REVERT: C 158 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: D 53 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8250 (tptp) REVERT: D 158 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9189 (m-80) REVERT: D 230 PHE cc_start: 0.7684 (t80) cc_final: 0.7282 (t80) REVERT: E 43 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: E 45 TYR cc_start: 0.8188 (m-80) cc_final: 0.7690 (m-80) REVERT: E 63 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9181 (mm) REVERT: E 158 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9142 (m-80) REVERT: E 202 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8758 (tpp-160) outliers start: 81 outliers final: 55 residues processed: 285 average time/residue: 0.1589 time to fit residues: 65.5897 Evaluate side-chains 279 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 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 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE 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 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE 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 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 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 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 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 149 ASN 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 202 ARG 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 39 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 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 = 0.3789 r_free = 0.3789 target = 0.123804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099154 restraints weight = 15511.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102368 restraints weight = 6864.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104476 restraints weight = 4220.461| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8244 Z= 0.189 Angle : 0.698 12.827 11112 Z= 0.332 Chirality : 0.043 0.170 1260 Planarity : 0.003 0.039 1272 Dihedral : 19.176 106.483 1529 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 9.93 % Allowed : 29.53 % Favored : 60.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 896 helix: 0.85 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 196 HIS 0.001 0.001 HIS D 22 PHE 0.021 0.001 PHE D 94 TYR 0.011 0.001 TYR C 214 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 219 time to evaluate : 0.818 Fit side-chains REVERT: A 43 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: A 45 TYR cc_start: 0.8096 (m-80) cc_final: 0.7561 (m-80) REVERT: A 63 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9000 (mt) REVERT: A 158 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.9117 (m-80) REVERT: C 43 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7596 (pp20) REVERT: C 45 TYR cc_start: 0.8120 (m-80) cc_final: 0.7580 (m-80) REVERT: C 54 TRP cc_start: 0.7026 (p-90) cc_final: 0.6812 (p-90) REVERT: C 63 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8991 (mt) REVERT: C 158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9104 (m-80) REVERT: C 220 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8701 (mm) REVERT: D 45 TYR cc_start: 0.8158 (m-80) cc_final: 0.7743 (m-80) REVERT: D 63 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9069 (mm) REVERT: D 158 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9125 (m-80) REVERT: E 40 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.8822 (p) REVERT: E 43 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: E 45 TYR cc_start: 0.8108 (m-80) cc_final: 0.7567 (m-80) REVERT: E 63 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9201 (mm) REVERT: E 158 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9095 (m-80) outliers start: 81 outliers final: 60 residues processed: 277 average time/residue: 0.1455 time to fit residues: 58.9886 Evaluate side-chains 282 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 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 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 43 GLU 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 127 ILE 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 D residue 228 ASN 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 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 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** A 228 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099528 restraints weight = 16085.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102909 restraints weight = 7238.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105064 restraints weight = 4485.386| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8244 Z= 0.174 Angle : 0.702 13.443 11112 Z= 0.332 Chirality : 0.043 0.173 1260 Planarity : 0.003 0.038 1272 Dihedral : 18.099 106.035 1528 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 9.56 % Allowed : 30.51 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 896 helix: 0.67 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 196 HIS 0.002 0.000 HIS D 52 PHE 0.020 0.001 PHE D 94 TYR 0.010 0.001 TYR E 214 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 43 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: A 158 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9083 (m-80) REVERT: A 220 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 230 PHE cc_start: 0.7726 (t80) cc_final: 0.7504 (t80) REVERT: C 40 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 43 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: C 54 TRP cc_start: 0.6963 (p-90) cc_final: 0.6747 (p-90) REVERT: C 158 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9092 (m-80) REVERT: C 220 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 45 TYR cc_start: 0.8147 (m-80) cc_final: 0.7764 (m-80) REVERT: D 63 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8885 (mm) REVERT: D 149 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8431 (p0) REVERT: D 158 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9117 (m-80) REVERT: D 220 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8632 (mt) REVERT: E 40 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.8888 (p) REVERT: E 43 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: E 60 ASP cc_start: 0.8816 (t70) cc_final: 0.8295 (t0) REVERT: E 63 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9175 (mm) REVERT: E 149 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (p0) REVERT: E 158 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.9098 (m-80) REVERT: E 201 MET cc_start: 0.8494 (ttp) cc_final: 0.8203 (ttp) REVERT: E 220 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8470 (mt) outliers start: 78 outliers final: 50 residues processed: 273 average time/residue: 0.1502 time to fit residues: 58.8922 Evaluate side-chains 279 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 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 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 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 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 149 ASN 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3805 r_free = 0.3805 target = 0.124721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099707 restraints weight = 15500.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102961 restraints weight = 6966.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105092 restraints weight = 4305.061| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8244 Z= 0.199 Angle : 0.718 13.734 11112 Z= 0.341 Chirality : 0.043 0.174 1260 Planarity : 0.003 0.034 1272 Dihedral : 17.837 108.090 1524 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 8.95 % Allowed : 31.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 896 helix: 0.79 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.64 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 212 HIS 0.001 0.000 HIS D 22 PHE 0.018 0.001 PHE D 94 TYR 0.016 0.002 TYR E 159 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 43 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: A 158 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: A 220 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8477 (mt) REVERT: C 40 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8776 (p) REVERT: C 43 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: C 54 TRP cc_start: 0.6933 (p-90) cc_final: 0.6682 (p-90) REVERT: C 158 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9067 (m-80) REVERT: C 220 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8508 (mt) REVERT: D 45 TYR cc_start: 0.8150 (m-80) cc_final: 0.7786 (m-80) REVERT: D 63 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8949 (mm) REVERT: D 158 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9100 (m-80) REVERT: E 40 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8786 (p) REVERT: E 43 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: E 60 ASP cc_start: 0.8841 (t70) cc_final: 0.8369 (t0) REVERT: E 63 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9189 (mm) REVERT: E 158 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: E 201 MET cc_start: 0.8522 (ttp) cc_final: 0.8243 (ttp) REVERT: E 220 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8484 (mt) outliers start: 73 outliers final: 53 residues processed: 263 average time/residue: 0.1497 time to fit residues: 57.0353 Evaluate side-chains 273 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101125 restraints weight = 15670.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104400 restraints weight = 6978.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106621 restraints weight = 4305.411| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8244 Z= 0.182 Angle : 0.717 13.210 11112 Z= 0.341 Chirality : 0.043 0.184 1260 Planarity : 0.003 0.031 1272 Dihedral : 17.257 105.434 1518 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 8.46 % Allowed : 32.97 % Favored : 58.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 896 helix: 0.78 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.63 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 196 HIS 0.002 0.000 HIS D 52 PHE 0.018 0.001 PHE D 94 TYR 0.009 0.001 TYR C 214 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 0.807 Fit side-chains REVERT: A 40 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8730 (p) REVERT: A 43 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7646 (pp20) REVERT: A 158 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9039 (m-80) REVERT: A 220 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8450 (mt) REVERT: C 40 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 73 MET cc_start: 0.6474 (tpt) cc_final: 0.6220 (tpt) REVERT: C 154 MET cc_start: 0.8281 (tpt) cc_final: 0.8071 (tpt) REVERT: C 158 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9050 (m-80) REVERT: C 220 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8371 (mt) REVERT: D 45 TYR cc_start: 0.8170 (m-80) cc_final: 0.7829 (m-80) REVERT: D 63 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8872 (mm) REVERT: D 158 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.9080 (m-80) REVERT: D 220 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8413 (mt) REVERT: E 40 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8747 (p) REVERT: E 43 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7639 (pp20) REVERT: E 45 TYR cc_start: 0.8045 (m-80) cc_final: 0.7488 (m-80) REVERT: E 60 ASP cc_start: 0.8842 (t70) cc_final: 0.8374 (t0) REVERT: E 158 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: E 201 MET cc_start: 0.8466 (ttp) cc_final: 0.8254 (ttt) REVERT: E 220 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 69 outliers final: 46 residues processed: 257 average time/residue: 0.1537 time to fit residues: 57.2577 Evaluate side-chains 263 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 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 C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL 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 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 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP 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 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 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101649 restraints weight = 15473.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104963 restraints weight = 6954.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107177 restraints weight = 4300.050| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8244 Z= 0.177 Angle : 0.730 12.877 11112 Z= 0.344 Chirality : 0.044 0.331 1260 Planarity : 0.003 0.029 1272 Dihedral : 16.802 99.957 1516 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 7.72 % Allowed : 33.46 % Favored : 58.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 896 helix: 0.60 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.46 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 196 HIS 0.001 0.000 HIS E 52 PHE 0.017 0.001 PHE D 94 TYR 0.009 0.001 TYR E 214 ARG 0.002 0.000 ARG A 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 0.843 Fit side-chains REVERT: A 40 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 43 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: A 81 LYS cc_start: 0.8809 (tptm) cc_final: 0.8418 (mmmt) REVERT: A 158 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: A 220 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 40 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 43 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7657 (pp20) REVERT: C 73 MET cc_start: 0.6419 (tpt) cc_final: 0.6184 (tpt) REVERT: C 81 LYS cc_start: 0.8818 (tptm) cc_final: 0.8439 (mmmt) REVERT: C 158 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9072 (m-80) REVERT: D 45 TYR cc_start: 0.8203 (m-80) cc_final: 0.7877 (m-80) REVERT: D 63 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8869 (mm) REVERT: D 81 LYS cc_start: 0.8876 (tptm) cc_final: 0.8455 (mmmt) REVERT: D 158 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9125 (m-80) REVERT: E 40 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8800 (p) REVERT: E 43 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: E 81 LYS cc_start: 0.8865 (tptm) cc_final: 0.8438 (mmmt) REVERT: E 154 MET cc_start: 0.7777 (tpt) cc_final: 0.7550 (tpt) REVERT: E 158 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8914 (m-80) REVERT: E 220 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8385 (mt) outliers start: 63 outliers final: 46 residues processed: 246 average time/residue: 0.1543 time to fit residues: 55.1282 Evaluate side-chains 254 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 85 PHE 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 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 C residue 19 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 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 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 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 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 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 = 0.3827 r_free = 0.3827 target = 0.125620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100583 restraints weight = 15733.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103965 restraints weight = 7012.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106156 restraints weight = 4325.820| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8244 Z= 0.191 Angle : 0.728 12.701 11112 Z= 0.347 Chirality : 0.044 0.292 1260 Planarity : 0.003 0.028 1272 Dihedral : 16.648 102.612 1516 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 7.11 % Allowed : 34.19 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 896 helix: 0.68 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.08 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 54 HIS 0.001 0.000 HIS D 22 PHE 0.017 0.001 PHE E 94 TYR 0.010 0.001 TYR A 214 ARG 0.002 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2596.07 seconds wall clock time: 47 minutes 18.24 seconds (2838.24 seconds total)