Starting phenix.real_space_refine on Fri Sep 11 06:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxo_21446/09_2026/6vxo_21446.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 24 5.16 5 C 5548 2.51 5 N 1184 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "E" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.46, per 1000 atoms: 0.18 Number of scatterers: 8048 At special positions: 0 Unit cell: (123.654, 123.654, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 12 15.00 O 1280 8.00 N 1184 7.00 C 5548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 373.6 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 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: 0.85 Time building geometry restraints manager: 0.93 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: 4051 24.08 - 48.16: 562 48.16 - 72.24: 159 72.24 - 96.32: 44 96.32 - 120.40: 12 Dihedral angle restraints: 4828 sinusoidal: 2160 harmonic: 2668 Sorted by residual: dihedral pdb=" CA VAL C 109 " pdb=" C VAL C 109 " pdb=" N GLU C 110 " pdb=" CA GLU C 110 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N ASN E 236 " pdb=" CA ASN E 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 235 " pdb=" C VAL D 235 " pdb=" N ASN D 236 " pdb=" CA ASN D 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 587 0.027 - 0.053: 338 0.053 - 0.079: 207 0.079 - 0.106: 93 0.106 - 0.132: 35 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA VAL A 235 " pdb=" N VAL A 235 " pdb=" C VAL A 235 " pdb=" CB VAL A 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 235 " pdb=" N VAL D 235 " pdb=" C VAL D 235 " pdb=" CB VAL D 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL C 235 " pdb=" N VAL C 235 " pdb=" C VAL C 235 " pdb=" CB VAL C 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1257 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE D 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE D 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE C 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 234 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ILE A 234 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 234 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 235 " -0.010 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 307 2.68 - 3.24: 8646 3.24 - 3.79: 12731 3.79 - 4.35: 15410 4.35 - 4.90: 25309 Nonbonded interactions: 62403 Sorted by model distance: nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR E 214 " pdb=" OG SER E 217 " model vdw 2.126 3.040 nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 217 " model vdw 2.126 3.040 nonbonded pdb=" O PHE E 161 " pdb=" OH TYR E 214 " model vdw 2.219 3.040 ... (remaining 62398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 302) selection = chain 'C' selection = (chain 'D' and resid 15 through 302) selection = (chain 'E' and resid 15 through 302) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.950 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.097 8244 Z= 0.586 Angle : 1.401 11.619 11112 Z= 0.585 Chirality : 0.047 0.132 1260 Planarity : 0.005 0.035 1272 Dihedral : 24.434 120.396 3084 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.17 % Favored : 87.39 % Rotamer: Outliers : 21.57 % Allowed : 21.08 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.24), residues: 896 helix: -1.88 (0.17), residues: 640 sheet: None (None), residues: 0 loop : -4.16 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 122 TYR 0.007 0.001 TYR A 159 PHE 0.017 0.002 PHE C 205 TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.01229 / 0.59 ( 8244) covalent geometry : angle 1.40070 / 0.58 (11112) hydrogen bonds : bond 0.17884 / 11.90 ( 428) hydrogen bonds : angle 7.61056 / 5.58 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 207 time to evaluate : 0.182 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: 0.7605 (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: 0.0586 time to fit residues: 29.4409 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN 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 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 = 0.3737 r_free = 0.3737 target = 0.120266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095608 restraints weight = 16083.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098749 restraints weight = 7147.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100811 restraints weight = 4395.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101912 restraints weight = 3299.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102827 restraints weight = 2809.013| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8244 Z= 0.141 Angle : 0.622 5.962 11112 Z= 0.320 Chirality : 0.041 0.155 1260 Planarity : 0.003 0.020 1272 Dihedral : 22.936 105.456 1684 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 9.56 % Allowed : 23.77 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.28), residues: 896 helix: 0.24 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.89 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.011 0.001 TYR D 214 PHE 0.015 0.001 PHE E 205 TRP 0.011 0.001 TRP E 65 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8244) covalent geometry : angle 0.62228 / 0.32 (11112) hydrogen bonds : bond 0.04346 / 2.87 ( 428) hydrogen bonds : angle 4.27567 / 3.12 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 220 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8334 (m-80) cc_final: 0.7990 (m-80) REVERT: A 53 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8138 (tptp) REVERT: A 65 TRP cc_start: 0.8035 (m100) cc_final: 0.7686 (t-100) REVERT: A 207 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 45 TYR cc_start: 0.8345 (m-80) cc_final: 0.7999 (m-80) REVERT: C 65 TRP cc_start: 0.8005 (m100) cc_final: 0.7657 (t-100) REVERT: C 207 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7570 (mm-30) REVERT: D 45 TYR cc_start: 0.8359 (m-80) cc_final: 0.8019 (m-80) REVERT: D 49 TYR cc_start: 0.8342 (t80) cc_final: 0.8141 (t80) REVERT: D 53 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8086 (tptp) REVERT: D 65 TRP cc_start: 0.8001 (m100) cc_final: 0.7640 (t-100) REVERT: D 207 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 45 TYR cc_start: 0.8362 (m-80) cc_final: 0.8047 (m-80) REVERT: E 65 TRP cc_start: 0.8069 (m100) cc_final: 0.7708 (t-100) REVERT: E 207 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7567 (mm-30) outliers start: 78 outliers final: 39 residues processed: 286 average time/residue: 0.0532 time to fit residues: 23.3948 Evaluate side-chains 251 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN C 228 ASN D 228 ASN E 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096322 restraints weight = 15840.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099430 restraints weight = 7257.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101458 restraints weight = 4532.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102614 restraints weight = 3431.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103447 restraints weight = 2936.850| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8244 Z= 0.128 Angle : 0.622 7.622 11112 Z= 0.315 Chirality : 0.043 0.164 1260 Planarity : 0.003 0.019 1272 Dihedral : 21.012 102.388 1477 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 10.78 % Allowed : 26.47 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.30), residues: 896 helix: 0.73 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.004 0.001 TYR E 214 PHE 0.025 0.001 PHE C 94 TRP 0.009 0.001 TRP E 65 HIS 0.001 0.000 HIS E 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8244) covalent geometry : angle 0.62177 / 0.32 (11112) hydrogen bonds : bond 0.04070 / 2.66 ( 428) hydrogen bonds : angle 3.96723 / 2.87 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 231 time to evaluate : 0.360 Fit side-chains REVERT: A 45 TYR cc_start: 0.8198 (m-80) cc_final: 0.7815 (m-80) REVERT: A 63 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9171 (mm) REVERT: A 65 TRP cc_start: 0.7937 (m100) cc_final: 0.7578 (t-100) REVERT: A 158 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9133 (m-80) REVERT: A 202 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8794 (tpp-160) REVERT: A 207 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 45 TYR cc_start: 0.8228 (m-80) cc_final: 0.7839 (m-80) REVERT: C 63 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9162 (mm) REVERT: C 65 TRP cc_start: 0.7940 (m100) cc_final: 0.7536 (t-100) REVERT: C 73 MET cc_start: 0.6454 (tpt) cc_final: 0.6201 (tpt) REVERT: C 158 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9175 (m-80) REVERT: C 202 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8858 (tpp-160) REVERT: C 207 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 45 TYR cc_start: 0.8193 (m-80) cc_final: 0.7811 (m-80) REVERT: D 63 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9173 (mm) REVERT: D 65 TRP cc_start: 0.8034 (m100) cc_final: 0.7727 (t-100) REVERT: D 158 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9149 (m-80) REVERT: D 202 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8863 (tpp-160) REVERT: D 207 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7531 (mm-30) REVERT: E 45 TYR cc_start: 0.8258 (m-80) cc_final: 0.7880 (m-80) REVERT: E 63 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9195 (mm) REVERT: E 65 TRP cc_start: 0.8040 (m100) cc_final: 0.7788 (t-100) REVERT: E 158 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9136 (m-80) REVERT: E 202 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (tpp-160) REVERT: E 207 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7521 (mm-30) outliers start: 88 outliers final: 51 residues processed: 302 average time/residue: 0.0629 time to fit residues: 28.3686 Evaluate side-chains 262 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 202 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 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 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 189 GLN 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 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 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 202 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.121373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096789 restraints weight = 15997.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099978 restraints weight = 7111.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102117 restraints weight = 4359.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103338 restraints weight = 3267.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103971 restraints weight = 2791.000| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8244 Z= 0.130 Angle : 0.650 12.476 11112 Z= 0.323 Chirality : 0.043 0.164 1260 Planarity : 0.003 0.024 1272 Dihedral : 19.892 96.110 1474 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 11.64 % Allowed : 25.86 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.30), residues: 896 helix: 0.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 47 TYR 0.010 0.001 TYR A 214 PHE 0.029 0.001 PHE E 94 TRP 0.009 0.001 TRP A 65 HIS 0.002 0.001 HIS D 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8244) covalent geometry : angle 0.65011 / 0.32 (11112) hydrogen bonds : bond 0.03984 / 2.59 ( 428) hydrogen bonds : angle 3.88920 / 2.80 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 217 time to evaluate : 0.291 Fit side-chains REVERT: A 45 TYR cc_start: 0.8210 (m-80) cc_final: 0.7780 (m-80) REVERT: A 63 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9146 (mm) REVERT: A 65 TRP cc_start: 0.8008 (m100) cc_final: 0.7789 (t-100) REVERT: A 158 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9061 (m-80) REVERT: A 207 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7575 (mm-30) REVERT: C 45 TYR cc_start: 0.8229 (m-80) cc_final: 0.7786 (m-80) REVERT: C 53 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8332 (tptp) REVERT: C 63 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9122 (mm) REVERT: C 65 TRP cc_start: 0.8015 (m100) cc_final: 0.7663 (t-100) REVERT: C 73 MET cc_start: 0.6358 (tpt) cc_final: 0.6099 (tpt) REVERT: C 138 ASP cc_start: 0.8237 (t0) cc_final: 0.8014 (t0) REVERT: C 158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9143 (m-80) REVERT: C 202 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8815 (tpp-160) REVERT: C 207 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 63 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9113 (mm) REVERT: D 65 TRP cc_start: 0.8039 (m100) cc_final: 0.7623 (t-100) REVERT: D 138 ASP cc_start: 0.8170 (t0) cc_final: 0.7960 (t0) REVERT: D 158 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9113 (m-80) REVERT: D 202 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8836 (tpp-160) REVERT: D 207 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7526 (mm-30) REVERT: E 45 TYR cc_start: 0.8239 (m-80) cc_final: 0.7805 (m-80) REVERT: E 65 TRP cc_start: 0.8016 (m100) cc_final: 0.7658 (t-100) REVERT: E 154 MET cc_start: 0.8453 (tpt) cc_final: 0.8238 (tpt) REVERT: E 158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9039 (m-80) REVERT: E 202 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8818 (tpp-160) REVERT: E 207 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7529 (mm-30) outliers start: 95 outliers final: 68 residues processed: 288 average time/residue: 0.0587 time to fit residues: 25.4294 Evaluate side-chains 286 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 208 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 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 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 202 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096035 restraints weight = 15869.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099161 restraints weight = 7192.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101234 restraints weight = 4487.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102389 restraints weight = 3398.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103041 restraints weight = 2911.648| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8244 Z= 0.151 Angle : 0.664 12.559 11112 Z= 0.326 Chirality : 0.044 0.165 1260 Planarity : 0.003 0.026 1272 Dihedral : 19.262 93.850 1462 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 10.42 % Allowed : 28.19 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 896 helix: 0.87 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.93 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 202 TYR 0.012 0.001 TYR A 214 PHE 0.024 0.001 PHE E 94 TRP 0.012 0.001 TRP D 65 HIS 0.001 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8244) covalent geometry : angle 0.66385 / 0.33 (11112) hydrogen bonds : bond 0.04080 / 2.67 ( 428) hydrogen bonds : angle 3.81100 / 2.73 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 216 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7596 (pp20) REVERT: A 45 TYR cc_start: 0.8214 (m-80) cc_final: 0.7787 (m-80) REVERT: A 63 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9144 (mm) REVERT: A 158 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9169 (m-80) REVERT: A 207 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 45 TYR cc_start: 0.8217 (m-80) cc_final: 0.7731 (m-80) REVERT: C 63 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9148 (mm) REVERT: C 138 ASP cc_start: 0.8249 (t0) cc_final: 0.8040 (t0) REVERT: C 158 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9149 (m-80) REVERT: C 207 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7593 (mm-30) REVERT: D 158 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9189 (m-80) REVERT: D 207 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 43 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: E 45 TYR cc_start: 0.8227 (m-80) cc_final: 0.7782 (m-80) REVERT: E 65 TRP cc_start: 0.8011 (m100) cc_final: 0.7718 (t-100) REVERT: E 106 LEU cc_start: 0.8948 (tp) cc_final: 0.8744 (tt) REVERT: E 158 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9194 (m-80) REVERT: E 202 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8805 (tpp-160) REVERT: E 207 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7504 (mm-30) REVERT: E 220 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8689 (mm) outliers start: 85 outliers final: 69 residues processed: 279 average time/residue: 0.0545 time to fit residues: 23.1952 Evaluate side-chains 289 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 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 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 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 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 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 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 1 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098512 restraints weight = 15653.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101754 restraints weight = 6920.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103897 restraints weight = 4235.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105074 restraints weight = 3170.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105889 restraints weight = 2704.402| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8244 Z= 0.119 Angle : 0.674 13.001 11112 Z= 0.323 Chirality : 0.043 0.169 1260 Planarity : 0.003 0.029 1272 Dihedral : 17.893 87.451 1460 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 10.29 % Allowed : 29.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 896 helix: 0.83 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 119 TYR 0.011 0.001 TYR E 214 PHE 0.023 0.001 PHE E 94 TRP 0.007 0.001 TRP A 196 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8244) covalent geometry : angle 0.67423 / 0.32 (11112) hydrogen bonds : bond 0.03833 / 2.49 ( 428) hydrogen bonds : angle 3.70088 / 2.64 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 227 time to evaluate : 0.306 Fit side-chains REVERT: A 45 TYR cc_start: 0.8115 (m-80) cc_final: 0.7648 (m-80) REVERT: A 63 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 158 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.9092 (m-80) REVERT: C 43 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: C 45 TYR cc_start: 0.8125 (m-80) cc_final: 0.7620 (m-80) REVERT: C 63 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9154 (mm) REVERT: C 158 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9111 (m-80) REVERT: C 230 PHE cc_start: 0.7668 (t80) cc_final: 0.7239 (t80) REVERT: D 45 TYR cc_start: 0.8212 (m-80) cc_final: 0.7846 (m-80) REVERT: D 158 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9118 (m-80) REVERT: E 40 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.8819 (p) REVERT: E 43 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: E 45 TYR cc_start: 0.8096 (m-80) cc_final: 0.7609 (m-80) REVERT: E 65 TRP cc_start: 0.7981 (m100) cc_final: 0.7736 (t-100) REVERT: E 106 LEU cc_start: 0.8880 (tp) cc_final: 0.8654 (tt) REVERT: E 158 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.9147 (m-80) REVERT: E 202 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8796 (tpp-160) outliers start: 84 outliers final: 61 residues processed: 287 average time/residue: 0.0566 time to fit residues: 24.4331 Evaluate side-chains 281 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 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 26 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 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 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097591 restraints weight = 15822.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100847 restraints weight = 6997.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102992 restraints weight = 4313.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104194 restraints weight = 3248.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104984 restraints weight = 2783.099| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8244 Z= 0.135 Angle : 0.732 12.957 11112 Z= 0.347 Chirality : 0.044 0.167 1260 Planarity : 0.003 0.039 1272 Dihedral : 17.417 81.968 1457 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 9.80 % Allowed : 30.51 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.29), residues: 896 helix: 0.88 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.60 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 202 TYR 0.012 0.001 TYR D 214 PHE 0.020 0.001 PHE E 94 TRP 0.010 0.001 TRP E 65 HIS 0.001 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8244) covalent geometry : angle 0.73231 / 0.35 (11112) hydrogen bonds : bond 0.03935 / 2.55 ( 428) hydrogen bonds : angle 3.76930 / 2.68 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: A 45 TYR cc_start: 0.8078 (m-80) cc_final: 0.7555 (m-80) REVERT: A 63 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9003 (mt) REVERT: A 158 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9119 (m-80) REVERT: A 220 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 40 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8713 (p) REVERT: C 43 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: C 45 TYR cc_start: 0.8084 (m-80) cc_final: 0.7539 (m-80) REVERT: C 158 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9089 (m-80) REVERT: C 220 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8580 (mt) REVERT: D 45 TYR cc_start: 0.8197 (m-80) cc_final: 0.7828 (m-80) REVERT: D 158 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.9144 (m-80) REVERT: D 220 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8681 (mm) REVERT: E 40 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.8858 (p) REVERT: E 43 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: E 106 LEU cc_start: 0.8967 (tp) cc_final: 0.8708 (tt) REVERT: E 158 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9123 (m-80) REVERT: E 202 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8807 (tpp-160) outliers start: 80 outliers final: 61 residues processed: 264 average time/residue: 0.0565 time to fit residues: 22.4463 Evaluate side-chains 277 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 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 26 THR 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 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 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 109 VAL 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 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 202 ARG 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 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095092 restraints weight = 15751.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098275 restraints weight = 6996.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100343 restraints weight = 4323.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101519 restraints weight = 3257.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102295 restraints weight = 2784.668| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8244 Z= 0.179 Angle : 0.758 13.779 11112 Z= 0.366 Chirality : 0.045 0.177 1260 Planarity : 0.003 0.034 1272 Dihedral : 17.519 86.573 1455 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 10.05 % Allowed : 30.88 % Favored : 59.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.28), residues: 896 helix: 0.79 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -2.69 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 202 TYR 0.012 0.002 TYR D 214 PHE 0.019 0.001 PHE E 94 TRP 0.009 0.001 TRP E 212 HIS 0.002 0.001 HIS E 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 8244) covalent geometry : angle 0.75786 / 0.37 (11112) hydrogen bonds : bond 0.04278 / 2.80 ( 428) hydrogen bonds : angle 3.99803 / 2.83 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 207 time to evaluate : 0.291 Fit side-chains REVERT: A 40 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 43 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: A 60 ASP cc_start: 0.8826 (t70) cc_final: 0.8421 (t0) REVERT: C 43 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: C 45 TYR cc_start: 0.8140 (m-80) cc_final: 0.7614 (m-80) REVERT: C 220 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8649 (mm) REVERT: D 45 TYR cc_start: 0.8240 (m-80) cc_final: 0.7898 (m-80) REVERT: D 158 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9192 (m-80) REVERT: E 40 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.8907 (p) REVERT: E 43 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: E 106 LEU cc_start: 0.8904 (tp) cc_final: 0.8630 (tt) REVERT: E 158 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9153 (m-80) outliers start: 82 outliers final: 69 residues processed: 264 average time/residue: 0.0574 time to fit residues: 22.9611 Evaluate side-chains 281 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 204 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 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 26 THR 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 26 THR 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 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 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 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 79 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 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 = 0.124637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099157 restraints weight = 15508.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102418 restraints weight = 6960.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104532 restraints weight = 4329.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105789 restraints weight = 3280.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106596 restraints weight = 2806.827| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8244 Z= 0.130 Angle : 0.734 13.070 11112 Z= 0.350 Chirality : 0.045 0.228 1260 Planarity : 0.003 0.031 1272 Dihedral : 16.386 82.404 1453 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 9.44 % Allowed : 31.62 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 896 helix: 0.91 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.008 0.001 TYR D 214 PHE 0.018 0.001 PHE E 94 TRP 0.006 0.001 TRP A 196 HIS 0.001 0.000 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8244) covalent geometry : angle 0.73399 / 0.35 (11112) hydrogen bonds : bond 0.03979 / 2.59 ( 428) hydrogen bonds : angle 3.83802 / 2.70 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 207 time to evaluate : 0.294 Fit side-chains REVERT: A 40 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 43 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: A 159 TYR cc_start: 0.8539 (t80) cc_final: 0.8229 (t80) REVERT: A 220 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 40 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8631 (p) REVERT: C 43 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7584 (pp20) REVERT: C 220 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8496 (mt) REVERT: D 45 TYR cc_start: 0.8224 (m-80) cc_final: 0.7906 (m-80) REVERT: D 63 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9015 (mm) REVERT: D 154 MET cc_start: 0.8304 (tpt) cc_final: 0.8099 (tpt) REVERT: D 158 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9075 (m-80) REVERT: D 220 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8593 (mt) REVERT: E 40 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8886 (p) REVERT: E 43 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7794 (pp20) REVERT: E 63 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9071 (mm) REVERT: E 106 LEU cc_start: 0.8979 (tp) cc_final: 0.8727 (tt) REVERT: E 158 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: E 159 TYR cc_start: 0.8606 (t80) cc_final: 0.8336 (t80) REVERT: E 220 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8554 (mt) outliers start: 77 outliers final: 57 residues processed: 263 average time/residue: 0.0565 time to fit residues: 22.4160 Evaluate side-chains 272 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 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 149 ASN Chi-restraints excluded: chain C residue 150 ILE 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 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 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099673 restraints weight = 15628.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102910 restraints weight = 6927.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105017 restraints weight = 4280.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106203 restraints weight = 3231.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107008 restraints weight = 2771.001| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8244 Z= 0.127 Angle : 0.735 12.936 11112 Z= 0.351 Chirality : 0.045 0.213 1260 Planarity : 0.003 0.030 1272 Dihedral : 15.539 76.416 1452 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 8.58 % Allowed : 33.58 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 896 helix: 0.75 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.37 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 202 TYR 0.009 0.001 TYR D 214 PHE 0.018 0.001 PHE E 94 TRP 0.009 0.001 TRP E 196 HIS 0.001 0.000 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8244) covalent geometry : angle 0.73518 / 0.35 (11112) hydrogen bonds : bond 0.03871 / 2.53 ( 428) hydrogen bonds : angle 3.79236 / 2.66 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 206 time to evaluate : 0.242 Fit side-chains REVERT: A 40 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8745 (p) REVERT: A 43 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: A 60 ASP cc_start: 0.8830 (t70) cc_final: 0.8444 (t0) REVERT: A 159 TYR cc_start: 0.8566 (t80) cc_final: 0.8219 (t80) REVERT: A 220 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8452 (mt) REVERT: C 40 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 43 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7624 (pp20) REVERT: C 220 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8452 (mt) REVERT: D 45 TYR cc_start: 0.8248 (m-80) cc_final: 0.7953 (m-80) REVERT: D 63 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8997 (mm) REVERT: D 158 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9093 (m-80) REVERT: D 220 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8661 (mt) REVERT: E 40 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8903 (p) REVERT: E 43 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: E 63 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9121 (mm) REVERT: E 106 LEU cc_start: 0.8857 (tp) cc_final: 0.8579 (tt) REVERT: E 149 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8355 (p0) REVERT: E 158 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.9038 (m-80) REVERT: E 220 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8488 (mt) outliers start: 70 outliers final: 52 residues processed: 256 average time/residue: 0.0609 time to fit residues: 23.1264 Evaluate side-chains 269 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 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 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 40 VAL 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 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099068 restraints weight = 15526.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102364 restraints weight = 6820.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104484 restraints weight = 4234.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105694 restraints weight = 3212.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106516 restraints weight = 2769.212| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8244 Z= 0.138 Angle : 0.739 13.401 11112 Z= 0.356 Chirality : 0.045 0.175 1260 Planarity : 0.003 0.029 1272 Dihedral : 15.271 76.450 1452 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 8.70 % Allowed : 33.82 % Favored : 57.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.29), residues: 896 helix: 0.80 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 202 TYR 0.011 0.001 TYR A 214 PHE 0.018 0.001 PHE E 94 TRP 0.011 0.001 TRP E 54 HIS 0.001 0.000 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8244) covalent geometry : angle 0.73930 / 0.36 (11112) hydrogen bonds : bond 0.03847 / 2.51 ( 428) hydrogen bonds : angle 3.76065 / 2.65 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.70 seconds wall clock time: 23 minutes 13.67 seconds (1393.67 seconds total)