Starting phenix.real_space_refine on Sat Jul 26 03:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxo_21446/07_2025/6vxo_21446.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 24 5.16 5 C 5548 2.51 5 N 1184 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: E Time building chain proxies: 5.91, per 1000 atoms: 0.73 Number of scatterers: 8048 At special positions: 0 Unit cell: (123.654, 123.654, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 12 15.00 O 1280 8.00 N 1184 7.00 C 5548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 4.283A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE A 56 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 148 through 169 removed outlier: 3.665A pdb=" N MET A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE C 56 " --> pdb=" O HIS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 122' Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 148 through 169 removed outlier: 3.664A pdb=" N MET C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 235 removed outlier: 3.960A pdb=" N PHE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE D 56 " --> pdb=" O HIS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 122' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 130 through 143 Processing helix chain 'D' and resid 148 through 169 removed outlier: 3.664A pdb=" N MET D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 43 removed outlier: 4.285A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE E 56 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 106 removed outlier: 3.546A pdb=" N TRP E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.892A pdb=" N LEU E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 122' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 148 through 169 removed outlier: 3.665A pdb=" N MET E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1084 1.30 - 1.43: 2299 1.43 - 1.55: 4723 1.55 - 1.68: 90 1.68 - 1.80: 48 Bond restraints: 8244 Sorted by residual: bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV C 302 " pdb=" O31 POV C 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV A 303 " pdb=" O31 POV A 303 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.28e+01 ... (remaining 8239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 10386 2.32 - 4.65: 483 4.65 - 6.97: 163 6.97 - 9.30: 48 9.30 - 11.62: 32 Bond angle restraints: 11112 Sorted by residual: angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 111.91 107.01 4.90 8.90e-01 1.26e+00 3.03e+01 angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL E 114 " pdb=" CA VAL E 114 " pdb=" C VAL E 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL D 114 " pdb=" CA VAL D 114 " pdb=" C VAL D 114 " ideal model delta sigma weight residual 111.91 107.04 4.87 8.90e-01 1.26e+00 3.00e+01 angle pdb=" O13 POV A 303 " pdb=" P POV A 303 " pdb=" O14 POV A 303 " ideal model delta sigma weight residual 121.11 109.49 11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 4071 24.08 - 48.16: 594 48.16 - 72.24: 175 72.24 - 96.32: 48 96.32 - 120.40: 12 Dihedral angle restraints: 4900 sinusoidal: 2232 harmonic: 2668 Sorted by residual: dihedral pdb=" CA VAL C 109 " pdb=" C VAL C 109 " pdb=" N GLU C 110 " pdb=" CA GLU C 110 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N ASN E 236 " pdb=" CA ASN E 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 235 " pdb=" C VAL D 235 " pdb=" N ASN D 236 " pdb=" CA ASN D 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 587 0.027 - 0.053: 338 0.053 - 0.079: 207 0.079 - 0.106: 93 0.106 - 0.132: 35 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA VAL A 235 " pdb=" N VAL A 235 " pdb=" C VAL A 235 " pdb=" CB VAL A 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 235 " pdb=" N VAL D 235 " pdb=" C VAL D 235 " pdb=" CB VAL D 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL C 235 " pdb=" N VAL C 235 " pdb=" C VAL C 235 " pdb=" CB VAL C 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1257 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE D 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE D 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE C 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 234 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ILE A 234 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 234 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 235 " -0.010 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 307 2.68 - 3.24: 8646 3.24 - 3.79: 12731 3.79 - 4.35: 15410 4.35 - 4.90: 25309 Nonbonded interactions: 62403 Sorted by model distance: nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR E 214 " pdb=" OG SER E 217 " model vdw 2.126 3.040 nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 217 " model vdw 2.126 3.040 nonbonded pdb=" O PHE E 161 " pdb=" OH TYR E 214 " model vdw 2.219 3.040 ... (remaining 62398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 240 or resid 301 through 302)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 240 or resid 301 through 302)) selection = (chain 'E' and (resid 15 through 240 or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.430 Find NCS groups from input model: 0.380 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.097 8244 Z= 0.586 Angle : 1.401 11.619 11112 Z= 0.585 Chirality : 0.047 0.132 1260 Planarity : 0.005 0.035 1272 Dihedral : 24.970 120.396 3156 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.17 % Favored : 87.39 % Rotamer: Outliers : 21.57 % Allowed : 21.08 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.24), residues: 896 helix: -1.88 (0.17), residues: 640 sheet: None (None), residues: 0 loop : -4.16 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 PHE 0.017 0.002 PHE C 205 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG E 122 Details of bonding type rmsd hydrogen bonds : bond 0.17884 ( 428) hydrogen bonds : angle 7.61056 ( 1284) covalent geometry : bond 0.01229 ( 8244) covalent geometry : angle 1.40070 (11112) *********************** 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 : 0.886 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8605 (m-80) cc_final: 0.8347 (m-80) REVERT: A 47 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: A 54 TRP cc_start: 0.7193 (p-90) cc_final: 0.6970 (p-90) REVERT: A 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 65 TRP cc_start: 0.8015 (m100) cc_final: 0.7668 (t-100) REVERT: A 70 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8263 (tp30) REVERT: A 103 GLU cc_start: 0.8881 (tp30) cc_final: 0.8587 (tp30) REVERT: A 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 45 TYR cc_start: 0.8575 (m-80) cc_final: 0.8319 (m-80) REVERT: C 47 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (ttm-80) REVERT: C 54 TRP cc_start: 0.7194 (p-90) cc_final: 0.6965 (p-90) REVERT: C 63 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9140 (mm) REVERT: C 65 TRP cc_start: 0.8002 (m100) cc_final: 0.7624 (t-100) REVERT: C 70 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8243 (tp30) REVERT: C 103 GLU cc_start: 0.8868 (tp30) cc_final: 0.8620 (tp30) REVERT: C 115 LEU cc_start: 0.8801 (mt) cc_final: 0.8526 (mt) REVERT: C 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7598 (t80) REVERT: D 45 TYR cc_start: 0.8603 (m-80) cc_final: 0.8339 (m-80) REVERT: D 47 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: D 54 TRP cc_start: 0.7218 (p-90) cc_final: 0.6990 (p-90) REVERT: D 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 65 TRP cc_start: 0.7986 (m100) cc_final: 0.7618 (t-100) REVERT: D 70 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8265 (tp30) REVERT: D 103 GLU cc_start: 0.8885 (tp30) cc_final: 0.8677 (tp30) REVERT: D 115 LEU cc_start: 0.8844 (mt) cc_final: 0.8593 (mt) REVERT: D 230 PHE cc_start: 0.7821 (t80) cc_final: 0.7598 (t80) REVERT: E 45 TYR cc_start: 0.8632 (m-80) cc_final: 0.8402 (m-80) REVERT: E 47 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (ttm-80) REVERT: E 54 TRP cc_start: 0.7227 (p-90) cc_final: 0.7024 (p-90) REVERT: E 63 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (mm) REVERT: E 65 TRP cc_start: 0.8109 (m100) cc_final: 0.7658 (t-100) REVERT: E 70 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8274 (tp30) REVERT: E 115 LEU cc_start: 0.8688 (mt) cc_final: 0.8449 (mt) REVERT: E 230 PHE cc_start: 0.7851 (t80) cc_final: 0.7623 (t80) outliers start: 176 outliers final: 141 residues processed: 336 average time/residue: 0.1479 time to fit residues: 72.1050 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 : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 170 GLN A 181 GLN A 189 GLN A 237 ASN C 90 ASN C 170 GLN C 181 GLN C 189 GLN C 237 ASN D 90 ASN D 170 GLN D 181 GLN D 237 ASN E 90 ASN E 170 GLN E 181 GLN E 237 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.120458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095681 restraints weight = 15844.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098805 restraints weight = 7117.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100871 restraints weight = 4406.595| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8244 Z= 0.136 Angle : 0.622 6.048 11112 Z= 0.319 Chirality : 0.041 0.155 1260 Planarity : 0.003 0.020 1272 Dihedral : 23.708 109.764 1756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 9.68 % Allowed : 23.53 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.29), residues: 896 helix: 0.27 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.001 0.001 HIS C 52 PHE 0.014 0.001 PHE D 205 TYR 0.012 0.002 TYR D 214 ARG 0.001 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 428) hydrogen bonds : angle 4.27667 ( 1284) covalent geometry : bond 0.00305 ( 8244) covalent geometry : angle 0.62210 (11112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 220 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8361 (m-80) cc_final: 0.8015 (m-80) REVERT: A 53 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8138 (tptp) REVERT: A 65 TRP cc_start: 0.8109 (m100) cc_final: 0.7739 (t-100) REVERT: A 207 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 45 TYR cc_start: 0.8369 (m-80) cc_final: 0.8013 (m-80) REVERT: C 54 TRP cc_start: 0.7023 (p-90) cc_final: 0.6817 (p-90) REVERT: C 65 TRP cc_start: 0.8073 (m100) cc_final: 0.7712 (t-100) REVERT: C 207 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 231 ILE cc_start: 0.8591 (mt) cc_final: 0.8390 (mt) REVERT: D 45 TYR cc_start: 0.8371 (m-80) cc_final: 0.7993 (m-80) REVERT: D 49 TYR cc_start: 0.8320 (t80) cc_final: 0.8117 (t80) REVERT: D 53 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8136 (tptp) REVERT: D 65 TRP cc_start: 0.8070 (m100) cc_final: 0.7697 (t-100) REVERT: D 138 ASP cc_start: 0.8290 (t0) cc_final: 0.8051 (t0) REVERT: D 207 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 45 TYR cc_start: 0.8411 (m-80) cc_final: 0.8085 (m-80) REVERT: E 65 TRP cc_start: 0.8147 (m100) cc_final: 0.7766 (t-100) REVERT: E 202 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8751 (tpp-160) REVERT: E 207 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7586 (mm-30) outliers start: 79 outliers final: 38 residues processed: 287 average time/residue: 0.1445 time to fit residues: 60.8150 Evaluate side-chains 252 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 ASN D 189 GLN D 228 ASN E 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097490 restraints weight = 15830.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100646 restraints weight = 7073.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102738 restraints weight = 4385.400| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8244 Z= 0.126 Angle : 0.622 7.666 11112 Z= 0.315 Chirality : 0.043 0.163 1260 Planarity : 0.003 0.018 1272 Dihedral : 22.021 109.743 1546 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 10.29 % Allowed : 25.74 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 896 helix: 0.74 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.16 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.001 0.000 HIS C 22 PHE 0.026 0.001 PHE C 94 TYR 0.004 0.001 TYR D 45 ARG 0.001 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 428) hydrogen bonds : angle 3.97483 ( 1284) covalent geometry : bond 0.00284 ( 8244) covalent geometry : angle 0.62215 (11112) *********************** 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 316 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 232 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8197 (m-80) cc_final: 0.7791 (m-80) REVERT: A 63 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9194 (mm) REVERT: A 73 MET cc_start: 0.6510 (tpt) cc_final: 0.6296 (tpt) REVERT: A 158 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9182 (m-80) REVERT: A 202 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (tpp-160) REVERT: A 207 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 45 TYR cc_start: 0.8221 (m-80) cc_final: 0.7811 (m-80) REVERT: C 55 LEU cc_start: 0.9058 (tp) cc_final: 0.8846 (pt) REVERT: C 65 TRP cc_start: 0.7946 (m100) cc_final: 0.7726 (t-100) REVERT: C 73 MET cc_start: 0.6590 (tpt) cc_final: 0.6362 (tpt) REVERT: C 158 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9176 (m-80) REVERT: C 207 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7584 (mm-30) REVERT: D 45 TYR cc_start: 0.8155 (m-80) cc_final: 0.7765 (m-80) REVERT: D 53 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8271 (tptp) REVERT: D 63 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9185 (mm) REVERT: D 65 TRP cc_start: 0.8091 (m100) cc_final: 0.7779 (t-100) REVERT: D 158 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9150 (m-80) REVERT: D 202 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8846 (tpp-160) REVERT: D 207 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7571 (mm-30) REVERT: E 45 TYR cc_start: 0.8251 (m-80) cc_final: 0.7849 (m-80) REVERT: E 63 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9203 (mm) REVERT: E 65 TRP cc_start: 0.8058 (m100) cc_final: 0.7801 (t-100) REVERT: E 138 ASP cc_start: 0.8243 (t0) cc_final: 0.8031 (t0) REVERT: E 158 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9096 (m-80) REVERT: E 201 MET cc_start: 0.8497 (ttt) cc_final: 0.8203 (ttp) REVERT: E 207 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7564 (mm-30) outliers start: 84 outliers final: 50 residues processed: 300 average time/residue: 0.1394 time to fit residues: 61.5650 Evaluate side-chains 257 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 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 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096509 restraints weight = 15666.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099703 restraints weight = 7041.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101808 restraints weight = 4405.584| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8244 Z= 0.133 Angle : 0.646 12.168 11112 Z= 0.322 Chirality : 0.043 0.162 1260 Planarity : 0.003 0.024 1272 Dihedral : 21.065 105.889 1540 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 10.78 % Allowed : 25.61 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.30), residues: 896 helix: 0.85 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.002 0.001 HIS A 52 PHE 0.030 0.001 PHE D 94 TYR 0.010 0.001 TYR A 214 ARG 0.001 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 428) hydrogen bonds : angle 3.91354 ( 1284) covalent geometry : bond 0.00301 ( 8244) covalent geometry : angle 0.64647 (11112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 213 time to evaluate : 0.892 Fit side-chains REVERT: A 45 TYR cc_start: 0.8211 (m-80) cc_final: 0.7751 (m-80) REVERT: A 63 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9124 (mm) REVERT: A 158 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9065 (m-80) REVERT: A 202 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8792 (tpp-160) REVERT: A 207 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7628 (mm-30) REVERT: C 45 TYR cc_start: 0.8169 (m-80) cc_final: 0.7738 (m-80) REVERT: C 63 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9094 (mm) REVERT: C 65 TRP cc_start: 0.8033 (m100) cc_final: 0.7687 (t-100) REVERT: C 73 MET cc_start: 0.6300 (tpt) cc_final: 0.6047 (tpt) REVERT: C 138 ASP cc_start: 0.8267 (t0) cc_final: 0.8042 (t0) REVERT: C 158 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.9123 (m-80) REVERT: D 53 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8243 (tptp) REVERT: D 63 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9142 (mm) REVERT: D 65 TRP cc_start: 0.8079 (m100) cc_final: 0.7670 (t-100) REVERT: D 158 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9159 (m-80) REVERT: D 207 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7578 (mm-30) REVERT: E 45 TYR cc_start: 0.8276 (m-80) cc_final: 0.7809 (m-80) REVERT: E 53 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8265 (tptp) REVERT: E 63 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9109 (mm) REVERT: E 65 TRP cc_start: 0.8099 (m100) cc_final: 0.7742 (t-100) REVERT: E 158 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9120 (m-80) REVERT: E 201 MET cc_start: 0.8549 (ttt) cc_final: 0.8240 (ttp) REVERT: E 207 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 88 outliers final: 65 residues processed: 282 average time/residue: 0.1425 time to fit residues: 59.6246 Evaluate side-chains 275 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 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 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 55 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 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 D residue 229 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097517 restraints weight = 15324.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100689 restraints weight = 6901.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102858 restraints weight = 4291.002| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8244 Z= 0.126 Angle : 0.655 12.779 11112 Z= 0.319 Chirality : 0.043 0.161 1260 Planarity : 0.003 0.028 1272 Dihedral : 20.201 107.470 1536 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 9.93 % Allowed : 28.31 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 896 helix: 0.73 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.80 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.001 0.000 HIS C 22 PHE 0.025 0.001 PHE D 94 TYR 0.011 0.001 TYR A 214 ARG 0.001 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 428) hydrogen bonds : angle 3.75808 ( 1284) covalent geometry : bond 0.00288 ( 8244) covalent geometry : angle 0.65482 (11112) *********************** 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 294 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 213 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: A 45 TYR cc_start: 0.8184 (m-80) cc_final: 0.7706 (m-80) REVERT: A 63 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 158 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9182 (m-80) REVERT: C 43 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: C 63 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9130 (mm) REVERT: C 138 ASP cc_start: 0.8246 (t0) cc_final: 0.8034 (t0) REVERT: C 158 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9146 (m-80) REVERT: D 53 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8281 (tptp) REVERT: D 63 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9156 (mm) REVERT: D 158 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9187 (m-80) REVERT: E 43 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: E 45 TYR cc_start: 0.8213 (m-80) cc_final: 0.7728 (m-80) REVERT: E 53 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8260 (tptp) REVERT: E 65 TRP cc_start: 0.8041 (m100) cc_final: 0.7752 (t-100) REVERT: E 106 LEU cc_start: 0.8937 (tp) cc_final: 0.8727 (tt) REVERT: E 158 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9173 (m-80) REVERT: E 201 MET cc_start: 0.8556 (ttt) cc_final: 0.8281 (ttp) REVERT: E 202 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8753 (tpp-160) outliers start: 81 outliers final: 63 residues processed: 272 average time/residue: 0.1482 time to fit residues: 59.2012 Evaluate side-chains 277 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 43 GLU 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 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 63 LEU 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 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 19 ILE 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 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 Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095850 restraints weight = 15765.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099004 restraints weight = 7078.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100981 restraints weight = 4385.967| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8244 Z= 0.185 Angle : 0.705 12.387 11112 Z= 0.347 Chirality : 0.045 0.165 1260 Planarity : 0.003 0.038 1272 Dihedral : 20.027 112.495 1536 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 10.29 % Allowed : 29.41 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 896 helix: 0.90 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 54 HIS 0.002 0.001 HIS A 171 PHE 0.021 0.002 PHE D 94 TYR 0.013 0.002 TYR C 214 ARG 0.001 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 428) hydrogen bonds : angle 3.95302 ( 1284) covalent geometry : bond 0.00435 ( 8244) covalent geometry : angle 0.70533 (11112) *********************** 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 290 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 206 time to evaluate : 0.919 Fit side-chains REVERT: A 45 TYR cc_start: 0.8204 (m-80) cc_final: 0.7745 (m-80) REVERT: A 63 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9022 (mt) REVERT: A 158 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9101 (m-80) REVERT: C 45 TYR cc_start: 0.8150 (m-80) cc_final: 0.7671 (m-80) REVERT: C 53 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8302 (tptp) REVERT: C 55 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8216 (pt) REVERT: C 63 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8985 (mt) REVERT: C 106 LEU cc_start: 0.8874 (tp) cc_final: 0.8670 (tt) REVERT: C 158 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.9132 (m-80) REVERT: D 45 TYR cc_start: 0.8254 (m-80) cc_final: 0.7854 (m-80) REVERT: D 63 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9135 (mm) REVERT: D 158 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.9221 (m-80) REVERT: E 40 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.8977 (p) REVERT: E 43 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: E 63 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9132 (mm) REVERT: E 65 TRP cc_start: 0.8131 (m100) cc_final: 0.7850 (t-100) REVERT: E 106 LEU cc_start: 0.8928 (tp) cc_final: 0.8674 (tt) REVERT: E 158 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9061 (m-80) REVERT: E 201 MET cc_start: 0.8517 (ttt) cc_final: 0.8210 (ttp) outliers start: 84 outliers final: 65 residues processed: 269 average time/residue: 0.1377 time to fit residues: 55.3034 Evaluate side-chains 277 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL 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 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 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 D residue 229 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 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 Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3748 r_free = 0.3748 target = 0.120567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096172 restraints weight = 15834.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099351 restraints weight = 7037.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101454 restraints weight = 4343.623| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8244 Z= 0.154 Angle : 0.696 11.747 11112 Z= 0.343 Chirality : 0.045 0.182 1260 Planarity : 0.003 0.039 1272 Dihedral : 19.314 113.435 1535 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 10.78 % Allowed : 30.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.29), residues: 896 helix: 0.94 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 54 HIS 0.001 0.001 HIS A 22 PHE 0.020 0.001 PHE D 94 TYR 0.009 0.001 TYR C 214 ARG 0.001 0.000 ARG D 202 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 428) hydrogen bonds : angle 3.89156 ( 1284) covalent geometry : bond 0.00364 ( 8244) covalent geometry : angle 0.69627 (11112) *********************** 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 303 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 0.809 Fit side-chains REVERT: A 43 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: A 45 TYR cc_start: 0.8171 (m-80) cc_final: 0.7699 (m-80) REVERT: A 63 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 159 TYR cc_start: 0.8519 (t80) cc_final: 0.8186 (t80) REVERT: C 45 TYR cc_start: 0.8194 (m-80) cc_final: 0.7703 (m-80) REVERT: C 53 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8357 (tptp) REVERT: C 106 LEU cc_start: 0.8823 (tp) cc_final: 0.8584 (tt) REVERT: C 159 TYR cc_start: 0.8548 (t80) cc_final: 0.8199 (t80) REVERT: D 45 TYR cc_start: 0.8207 (m-80) cc_final: 0.7836 (m-80) REVERT: D 63 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9194 (mm) REVERT: D 158 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9153 (m-80) REVERT: E 40 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.8900 (p) REVERT: E 43 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7624 (pp20) REVERT: E 45 TYR cc_start: 0.8149 (m-80) cc_final: 0.7641 (m-80) REVERT: E 63 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9156 (mm) REVERT: E 65 TRP cc_start: 0.8087 (m100) cc_final: 0.7860 (t-100) REVERT: E 106 LEU cc_start: 0.8955 (tp) cc_final: 0.8692 (tt) REVERT: E 158 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9108 (m-80) REVERT: E 201 MET cc_start: 0.8494 (ttt) cc_final: 0.8191 (ttp) outliers start: 88 outliers final: 76 residues processed: 276 average time/residue: 0.1443 time to fit residues: 58.9772 Evaluate side-chains 291 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 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 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 71 ILE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 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 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 142 MET 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 D residue 229 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 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 Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3773 r_free = 0.3773 target = 0.123076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098232 restraints weight = 15456.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101433 restraints weight = 6903.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103541 restraints weight = 4241.185| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8244 Z= 0.131 Angle : 0.700 13.835 11112 Z= 0.341 Chirality : 0.045 0.241 1260 Planarity : 0.003 0.040 1272 Dihedral : 18.382 110.661 1533 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 10.29 % Allowed : 31.62 % Favored : 58.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 896 helix: 0.64 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -2.32 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 54 HIS 0.001 0.000 HIS C 22 PHE 0.020 0.001 PHE D 94 TYR 0.010 0.001 TYR E 214 ARG 0.002 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 428) hydrogen bonds : angle 3.89903 ( 1284) covalent geometry : bond 0.00307 ( 8244) covalent geometry : angle 0.69997 (11112) *********************** 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 298 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 214 time to evaluate : 0.738 Fit side-chains REVERT: A 40 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 43 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: A 63 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8905 (mt) REVERT: A 159 TYR cc_start: 0.8472 (t80) cc_final: 0.8196 (t80) REVERT: A 202 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8849 (mmt180) REVERT: C 40 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8684 (p) REVERT: C 43 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7694 (pp20) REVERT: C 106 LEU cc_start: 0.8781 (tp) cc_final: 0.8563 (tt) REVERT: C 159 TYR cc_start: 0.8497 (t80) cc_final: 0.8193 (t80) REVERT: D 45 TYR cc_start: 0.8171 (m-80) cc_final: 0.7834 (m-80) REVERT: D 63 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8958 (mt) REVERT: D 158 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9114 (m-80) REVERT: D 230 PHE cc_start: 0.7608 (t80) cc_final: 0.7374 (t80) REVERT: E 40 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8804 (p) REVERT: E 43 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7598 (pp20) REVERT: E 63 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9049 (mt) REVERT: E 106 LEU cc_start: 0.9001 (tp) cc_final: 0.8715 (tt) REVERT: E 158 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: E 201 MET cc_start: 0.8438 (ttt) cc_final: 0.8159 (ttp) REVERT: E 202 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8753 (tpp-160) outliers start: 84 outliers final: 65 residues processed: 272 average time/residue: 0.1584 time to fit residues: 62.1832 Evaluate side-chains 283 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 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 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 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 40 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 127 ILE Chi-restraints excluded: chain D residue 142 MET 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 D residue 229 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098804 restraints weight = 15952.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102117 restraints weight = 7095.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104265 restraints weight = 4351.391| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8244 Z= 0.128 Angle : 0.714 13.285 11112 Z= 0.348 Chirality : 0.045 0.236 1260 Planarity : 0.003 0.037 1272 Dihedral : 17.737 109.196 1531 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 10.29 % Allowed : 31.74 % Favored : 57.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.28), residues: 896 helix: 0.41 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.15 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 65 HIS 0.001 0.000 HIS C 52 PHE 0.019 0.001 PHE D 94 TYR 0.010 0.001 TYR E 214 ARG 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 428) hydrogen bonds : angle 3.88039 ( 1284) covalent geometry : bond 0.00299 ( 8244) covalent geometry : angle 0.71366 (11112) *********************** 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 293 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 0.939 Fit side-chains REVERT: A 40 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 43 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: A 159 TYR cc_start: 0.8420 (t80) cc_final: 0.8192 (t80) REVERT: A 220 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 43 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: C 159 TYR cc_start: 0.8425 (t80) cc_final: 0.8162 (t80) REVERT: C 220 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8559 (mt) REVERT: D 45 TYR cc_start: 0.8161 (m-80) cc_final: 0.7834 (m-80) REVERT: D 63 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8859 (mt) REVERT: D 158 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9057 (m-80) REVERT: D 220 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8627 (mt) REVERT: D 230 PHE cc_start: 0.7580 (t80) cc_final: 0.7322 (t80) REVERT: E 40 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8757 (p) REVERT: E 43 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: E 63 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8920 (mt) REVERT: E 106 LEU cc_start: 0.8914 (tp) cc_final: 0.8639 (tt) REVERT: E 158 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.9051 (m-80) REVERT: E 201 MET cc_start: 0.8413 (ttt) cc_final: 0.8131 (ttp) REVERT: E 220 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8582 (mt) outliers start: 84 outliers final: 59 residues processed: 267 average time/residue: 0.1552 time to fit residues: 59.5665 Evaluate side-chains 275 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 118 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 118 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 229 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098592 restraints weight = 15719.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101875 restraints weight = 7050.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104017 restraints weight = 4377.033| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8244 Z= 0.135 Angle : 0.738 13.042 11112 Z= 0.359 Chirality : 0.045 0.326 1260 Planarity : 0.003 0.034 1272 Dihedral : 17.416 109.865 1528 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 8.70 % Allowed : 33.58 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.28), residues: 896 helix: 0.48 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 54 HIS 0.001 0.000 HIS A 22 PHE 0.019 0.001 PHE D 94 TYR 0.013 0.001 TYR A 214 ARG 0.002 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 428) hydrogen bonds : angle 3.88061 ( 1284) covalent geometry : bond 0.00318 ( 8244) covalent geometry : angle 0.73774 (11112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 204 time to evaluate : 0.859 Fit side-chains REVERT: A 40 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 43 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: A 159 TYR cc_start: 0.8420 (t80) cc_final: 0.8196 (t80) REVERT: A 220 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8548 (mt) REVERT: C 40 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8730 (p) REVERT: C 43 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: C 159 TYR cc_start: 0.8430 (t80) cc_final: 0.8132 (t80) REVERT: C 220 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8522 (mt) REVERT: D 45 TYR cc_start: 0.8179 (m-80) cc_final: 0.7855 (m-80) REVERT: D 158 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9010 (m-80) REVERT: D 220 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8557 (mt) REVERT: E 40 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8766 (p) REVERT: E 43 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7636 (pp20) REVERT: E 63 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8827 (mt) REVERT: E 106 LEU cc_start: 0.8873 (tp) cc_final: 0.8632 (tt) REVERT: E 158 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.9054 (m-80) REVERT: E 201 MET cc_start: 0.8425 (ttt) cc_final: 0.8144 (ttp) REVERT: E 220 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8579 (mt) REVERT: E 230 PHE cc_start: 0.7672 (t80) cc_final: 0.7410 (t80) outliers start: 71 outliers final: 56 residues processed: 255 average time/residue: 0.1526 time to fit residues: 56.6326 Evaluate side-chains 271 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 118 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 C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 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 229 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.0040 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101481 restraints weight = 15677.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104873 restraints weight = 6999.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107098 restraints weight = 4320.412| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8244 Z= 0.122 Angle : 0.731 12.886 11112 Z= 0.352 Chirality : 0.044 0.222 1260 Planarity : 0.003 0.033 1272 Dihedral : 16.391 102.130 1526 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.72 % Allowed : 34.80 % Favored : 57.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.28), residues: 896 helix: 0.68 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.43 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 54 HIS 0.001 0.000 HIS D 22 PHE 0.018 0.001 PHE D 94 TYR 0.010 0.001 TYR D 159 ARG 0.002 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 428) hydrogen bonds : angle 3.81005 ( 1284) covalent geometry : bond 0.00273 ( 8244) covalent geometry : angle 0.73092 (11112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.99 seconds wall clock time: 60 minutes 3.83 seconds (3603.83 seconds total)