Starting phenix.real_space_refine on Wed Mar 4 00:42:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2026/6vsc_21376.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.111 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6230 2.51 5 N 1610 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9670 Number of models: 1 Model: "" Number of chains: 5 Chain: "V" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "W" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "X" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Y" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Z" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.25 Number of scatterers: 9670 At special positions: 0 Unit cell: (101.01, 98.28, 76.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1780 8.00 N 1610 7.00 C 6230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 319.8 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'V' and resid 21 through 28 Processing helix chain 'V' and resid 29 through 53 Processing helix chain 'V' and resid 78 through 91 Processing helix chain 'V' and resid 92 through 96 Processing helix chain 'V' and resid 124 through 132 Processing helix chain 'V' and resid 160 through 178 removed outlier: 3.615A pdb=" N ALA V 170 " --> pdb=" O GLU V 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR V 178 " --> pdb=" O THR V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 217 removed outlier: 3.786A pdb=" N LYS V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 225 Processing helix chain 'V' and resid 238 through 240 No H-bonds generated for 'chain 'V' and resid 238 through 240' Processing helix chain 'V' and resid 241 through 246 Processing helix chain 'W' and resid 21 through 28 Processing helix chain 'W' and resid 29 through 53 Processing helix chain 'W' and resid 78 through 91 Processing helix chain 'W' and resid 92 through 96 Processing helix chain 'W' and resid 124 through 132 Processing helix chain 'W' and resid 160 through 178 removed outlier: 3.616A pdb=" N ALA W 170 " --> pdb=" O GLU W 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS W 171 " --> pdb=" O LEU W 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR W 178 " --> pdb=" O THR W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 217 removed outlier: 3.784A pdb=" N LYS W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 225 Processing helix chain 'W' and resid 238 through 240 No H-bonds generated for 'chain 'W' and resid 238 through 240' Processing helix chain 'W' and resid 241 through 246 Processing helix chain 'X' and resid 21 through 28 Processing helix chain 'X' and resid 29 through 53 Processing helix chain 'X' and resid 78 through 91 Processing helix chain 'X' and resid 92 through 96 Processing helix chain 'X' and resid 124 through 132 Processing helix chain 'X' and resid 160 through 178 removed outlier: 3.615A pdb=" N ALA X 170 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS X 171 " --> pdb=" O LEU X 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR X 178 " --> pdb=" O THR X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 217 removed outlier: 3.782A pdb=" N LYS X 210 " --> pdb=" O ALA X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 225 Processing helix chain 'X' and resid 238 through 240 No H-bonds generated for 'chain 'X' and resid 238 through 240' Processing helix chain 'X' and resid 241 through 246 Processing helix chain 'Y' and resid 21 through 28 Processing helix chain 'Y' and resid 29 through 53 Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 92 through 96 Processing helix chain 'Y' and resid 124 through 132 removed outlier: 6.025A pdb=" N ARG Y 130 " --> pdb=" O GLU Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 178 removed outlier: 3.612A pdb=" N ALA Y 170 " --> pdb=" O GLU Y 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR Y 178 " --> pdb=" O THR Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 removed outlier: 3.779A pdb=" N LYS Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 225 Processing helix chain 'Y' and resid 238 through 240 No H-bonds generated for 'chain 'Y' and resid 238 through 240' Processing helix chain 'Y' and resid 241 through 246 Processing helix chain 'Z' and resid 21 through 28 Processing helix chain 'Z' and resid 29 through 53 Processing helix chain 'Z' and resid 78 through 91 Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 124 through 132 Processing helix chain 'Z' and resid 160 through 178 removed outlier: 3.617A pdb=" N ALA Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS Z 171 " --> pdb=" O LEU Z 167 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Z 178 " --> pdb=" O THR Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 217 removed outlier: 3.785A pdb=" N LYS Z 210 " --> pdb=" O ALA Z 206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 225 Processing helix chain 'Z' and resid 238 through 240 No H-bonds generated for 'chain 'Z' and resid 238 through 240' Processing helix chain 'Z' and resid 241 through 246 Processing sheet with id=AA1, first strand: chain 'V' and resid 226 through 228 removed outlier: 4.168A pdb=" N TRP V 11 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR V 19 " --> pdb=" O PRO V 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU V 109 " --> pdb=" O ILE V 186 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE V 186 " --> pdb=" O GLU V 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 150 through 151 Processing sheet with id=AA3, first strand: chain 'W' and resid 226 through 228 removed outlier: 5.941A pdb=" N ASP W 9 " --> pdb=" O LEU W 110 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU W 110 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP W 11 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR W 19 " --> pdb=" O PRO W 100 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU W 109 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE W 186 " --> pdb=" O GLU W 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'X' and resid 226 through 228 removed outlier: 5.937A pdb=" N ASP X 9 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU X 110 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TRP X 11 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR X 19 " --> pdb=" O PRO X 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU X 109 " --> pdb=" O ILE X 186 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE X 186 " --> pdb=" O GLU X 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 150 through 151 Processing sheet with id=AA7, first strand: chain 'Y' and resid 226 through 228 removed outlier: 5.941A pdb=" N ASP Y 9 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU Y 110 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP Y 11 " --> pdb=" O VAL Y 108 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR Y 19 " --> pdb=" O PRO Y 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU Y 109 " --> pdb=" O ILE Y 186 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE Y 186 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'Z' and resid 226 through 228 removed outlier: 5.937A pdb=" N ASP Z 9 " --> pdb=" O LEU Z 110 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU Z 110 " --> pdb=" O ASP Z 9 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP Z 11 " --> pdb=" O VAL Z 108 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR Z 19 " --> pdb=" O PRO Z 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU Z 109 " --> pdb=" O ILE Z 186 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE Z 186 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 150 through 151 564 hydrogen bonds defined for protein. 1557 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: 1.74 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2284 1.33 - 1.47: 3464 1.47 - 1.62: 4082 1.62 - 1.76: 5 1.76 - 1.90: 85 Bond restraints: 9920 Sorted by residual: bond pdb=" CE1 HIS Z 83 " pdb=" NE2 HIS Z 83 " ideal model delta sigma weight residual 1.321 1.389 -0.068 1.00e-02 1.00e+04 4.66e+01 bond pdb=" CE1 HIS X 83 " pdb=" NE2 HIS X 83 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" CE1 HIS Y 83 " pdb=" NE2 HIS Y 83 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.29e+01 bond pdb=" CE1 HIS V 83 " pdb=" NE2 HIS V 83 " ideal model delta sigma weight residual 1.321 1.385 -0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" CE1 HIS W 83 " pdb=" NE2 HIS W 83 " ideal model delta sigma weight residual 1.321 1.382 -0.061 1.00e-02 1.00e+04 3.66e+01 ... (remaining 9915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 11665 3.41 - 6.81: 1516 6.81 - 10.22: 203 10.22 - 13.63: 34 13.63 - 17.03: 7 Bond angle restraints: 13425 Sorted by residual: angle pdb=" CA PRO V 121 " pdb=" N PRO V 121 " pdb=" CD PRO V 121 " ideal model delta sigma weight residual 112.00 99.20 12.80 1.40e+00 5.10e-01 8.36e+01 angle pdb=" CG ARG Y 164 " pdb=" CD ARG Y 164 " pdb=" NE ARG Y 164 " ideal model delta sigma weight residual 112.00 94.97 17.03 2.20e+00 2.07e-01 5.99e+01 angle pdb=" CG ARG W 164 " pdb=" CD ARG W 164 " pdb=" NE ARG W 164 " ideal model delta sigma weight residual 112.00 95.09 16.91 2.20e+00 2.07e-01 5.91e+01 angle pdb=" CG ARG V 164 " pdb=" CD ARG V 164 " pdb=" NE ARG V 164 " ideal model delta sigma weight residual 112.00 95.18 16.82 2.20e+00 2.07e-01 5.85e+01 angle pdb=" CG ARG X 164 " pdb=" CD ARG X 164 " pdb=" NE ARG X 164 " ideal model delta sigma weight residual 112.00 95.22 16.78 2.20e+00 2.07e-01 5.82e+01 ... (remaining 13420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4897 17.82 - 35.64: 713 35.64 - 53.45: 174 53.45 - 71.27: 52 71.27 - 89.09: 14 Dihedral angle restraints: 5850 sinusoidal: 2405 harmonic: 3445 Sorted by residual: dihedral pdb=" C MET Z 146 " pdb=" N MET Z 146 " pdb=" CA MET Z 146 " pdb=" CB MET Z 146 " ideal model delta harmonic sigma weight residual -122.60 -102.00 -20.60 0 2.50e+00 1.60e-01 6.79e+01 dihedral pdb=" C VAL Z 221 " pdb=" N VAL Z 221 " pdb=" CA VAL Z 221 " pdb=" CB VAL Z 221 " ideal model delta harmonic sigma weight residual -122.00 -142.46 20.46 0 2.50e+00 1.60e-01 6.69e+01 dihedral pdb=" N VAL Z 221 " pdb=" C VAL Z 221 " pdb=" CA VAL Z 221 " pdb=" CB VAL Z 221 " ideal model delta harmonic sigma weight residual 123.40 143.85 -20.45 0 2.50e+00 1.60e-01 6.69e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1099 0.161 - 0.321: 272 0.321 - 0.482: 52 0.482 - 0.642: 1 0.642 - 0.803: 6 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA VAL Z 221 " pdb=" N VAL Z 221 " pdb=" C VAL Z 221 " pdb=" CB VAL Z 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA VAL X 221 " pdb=" N VAL X 221 " pdb=" C VAL X 221 " pdb=" CB VAL X 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA VAL V 221 " pdb=" N VAL V 221 " pdb=" C VAL V 221 " pdb=" CB VAL V 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 1427 not shown) Planarity restraints: 1705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 178 " 0.030 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C TYR Y 178 " -0.106 2.00e-02 2.50e+03 pdb=" O TYR Y 178 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA Y 179 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 225 " -0.035 2.00e-02 2.50e+03 4.59e-02 3.69e+01 pdb=" CG PHE Z 225 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 225 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 225 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 225 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 225 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE Z 225 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 225 " 0.035 2.00e-02 2.50e+03 4.58e-02 3.67e+01 pdb=" CG PHE W 225 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE W 225 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE W 225 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE W 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE W 225 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE W 225 " 0.088 2.00e-02 2.50e+03 ... (remaining 1702 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 986 2.70 - 3.25: 9413 3.25 - 3.80: 18076 3.80 - 4.35: 24730 4.35 - 4.90: 38445 Nonbonded interactions: 91650 Sorted by model distance: nonbonded pdb=" NZ LYS V 67 " pdb=" OD1 ASP W 194 " model vdw 2.153 3.120 nonbonded pdb=" NZ LYS W 67 " pdb=" OD1 ASP Y 194 " model vdw 2.155 3.120 nonbonded pdb=" NZ LYS X 67 " pdb=" OD1 ASP Z 194 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP X 194 " pdb=" NZ LYS Y 67 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASP V 194 " pdb=" NZ LYS Z 67 " model vdw 2.186 3.120 ... (remaining 91645 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: 0.01 Found NCS groups: ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 individual isotropic 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.170 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 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 : 0.014 0.126 9920 Z= 0.919 Angle : 2.410 17.031 13425 Z= 1.576 Chirality : 0.153 0.803 1430 Planarity : 0.012 0.061 1705 Dihedral : 18.437 89.087 3630 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.73 % Allowed : 11.59 % Favored : 80.68 % Cbeta Deviations : 6.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.23), residues: 1155 helix: -2.12 (0.18), residues: 510 sheet: 0.21 (0.29), residues: 320 loop : -1.01 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.005 ARG Y 129 TYR 0.053 0.011 TYR X 140 PHE 0.088 0.016 PHE Z 225 TRP 0.047 0.012 TRP W 25 HIS 0.018 0.007 HIS W 58 Details of bonding type rmsd covalent geometry : bond 0.01383 ( 9920) covalent geometry : angle 2.41021 (13425) hydrogen bonds : bond 0.17554 ( 564) hydrogen bonds : angle 7.71179 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8897 (tm-30) REVERT: V 109 GLU cc_start: 0.8648 (pt0) cc_final: 0.8330 (pm20) REVERT: V 110 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6811 (mp) REVERT: V 130 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8244 (ttp-170) REVERT: V 147 ASP cc_start: 0.9198 (m-30) cc_final: 0.8951 (m-30) REVERT: V 153 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7276 (p0) REVERT: V 181 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8023 (mmtm) REVERT: V 184 GLN cc_start: 0.9078 (tt0) cc_final: 0.8779 (pm20) REVERT: V 196 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8965 (mt-10) REVERT: V 210 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9028 (tmmt) REVERT: W 30 ASN cc_start: 0.8802 (t0) cc_final: 0.8387 (t0) REVERT: W 105 VAL cc_start: 0.9154 (t) cc_final: 0.8913 (p) REVERT: W 123 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7886 (mp-120) REVERT: W 165 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8035 (mtm110) REVERT: W 181 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (mmtp) REVERT: W 205 ASP cc_start: 0.9150 (t0) cc_final: 0.8916 (t0) REVERT: X 33 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8704 (mtm110) REVERT: X 34 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8757 (tm-30) REVERT: X 130 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8435 (ttp-170) REVERT: X 181 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (mtpm) REVERT: X 184 GLN cc_start: 0.9169 (tt0) cc_final: 0.8840 (pm20) REVERT: Y 128 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8402 (mmp-170) REVERT: Y 129 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8489 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8365 (ttt180) REVERT: Y 147 ASP cc_start: 0.9174 (m-30) cc_final: 0.8589 (m-30) REVERT: Y 151 GLN cc_start: 0.9099 (mm110) cc_final: 0.8898 (tt0) REVERT: Y 165 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8156 (mtm110) REVERT: Y 181 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mmmt) REVERT: Y 184 GLN cc_start: 0.9202 (tt0) cc_final: 0.8904 (pm20) REVERT: Z 30 ASN cc_start: 0.8947 (t0) cc_final: 0.8514 (t0) REVERT: Z 109 GLU cc_start: 0.8653 (pt0) cc_final: 0.8355 (pm20) REVERT: Z 110 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7039 (mp) REVERT: Z 128 ARG cc_start: 0.8743 (tpt170) cc_final: 0.8513 (mmm160) REVERT: Z 151 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8879 (tt0) REVERT: Z 165 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7655 (mtm110) REVERT: Z 181 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mtpm) REVERT: Z 184 GLN cc_start: 0.9159 (tt0) cc_final: 0.8937 (pm20) REVERT: Z 210 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9079 (tmmt) outliers start: 80 outliers final: 13 residues processed: 405 average time/residue: 0.6315 time to fit residues: 270.7799 Evaluate side-chains 285 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 LYS Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 153 ASN Chi-restraints excluded: chain V residue 181 LYS Chi-restraints excluded: chain V residue 210 LYS Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 67 LYS Chi-restraints excluded: chain W residue 123 GLN Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain W residue 233 VAL Chi-restraints excluded: chain X residue 33 ARG Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 67 LYS Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 153 ASN Chi-restraints excluded: chain Z residue 181 LYS Chi-restraints excluded: chain Z residue 210 LYS Chi-restraints excluded: chain Z residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 247 HIS W 6 GLN W 247 HIS X 55 GLN X 247 HIS Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093984 restraints weight = 19181.484| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.19 r_work: 0.3323 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9920 Z= 0.189 Angle : 0.654 8.262 13425 Z= 0.344 Chirality : 0.044 0.148 1430 Planarity : 0.005 0.044 1705 Dihedral : 7.771 59.575 1371 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 5.60 % Allowed : 20.87 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1155 helix: -0.03 (0.21), residues: 535 sheet: -0.32 (0.26), residues: 360 loop : -0.88 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 149 TYR 0.020 0.002 TYR Y 157 PHE 0.020 0.002 PHE W 225 TRP 0.019 0.001 TRP X 156 HIS 0.004 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9920) covalent geometry : angle 0.65368 (13425) hydrogen bonds : bond 0.04231 ( 564) hydrogen bonds : angle 5.70377 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 342 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 147 ASP cc_start: 0.8209 (m-30) cc_final: 0.7955 (m-30) REVERT: V 169 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7307 (ttp-170) REVERT: V 216 MET cc_start: 0.8075 (mtm) cc_final: 0.7742 (mtp) REVERT: V 217 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8453 (ttm170) REVERT: W 30 ASN cc_start: 0.8233 (t0) cc_final: 0.7933 (t0) REVERT: W 102 TYR cc_start: 0.8258 (t80) cc_final: 0.7965 (t80) REVERT: W 129 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8171 (ttp-110) REVERT: W 165 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7409 (mtm110) REVERT: W 173 MET cc_start: 0.8201 (mmp) cc_final: 0.7979 (mmp) REVERT: W 219 ASP cc_start: 0.8210 (m-30) cc_final: 0.8003 (p0) REVERT: X 151 GLN cc_start: 0.8890 (tp40) cc_final: 0.8606 (tt0) REVERT: X 193 ASP cc_start: 0.8642 (t0) cc_final: 0.8331 (t0) REVERT: X 196 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8013 (mt-10) REVERT: X 210 LYS cc_start: 0.9197 (tmmt) cc_final: 0.8883 (tttm) REVERT: X 216 MET cc_start: 0.8053 (mtm) cc_final: 0.7802 (mtp) REVERT: Y 129 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7735 (ttm-80) REVERT: Y 196 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7943 (mt-10) REVERT: Y 216 MET cc_start: 0.8256 (mtm) cc_final: 0.7731 (mtp) REVERT: Z 147 ASP cc_start: 0.7986 (m-30) cc_final: 0.7713 (m-30) REVERT: Z 165 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.7053 (mtm110) REVERT: Z 193 ASP cc_start: 0.8374 (t0) cc_final: 0.7708 (t0) REVERT: Z 196 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7671 (mt-10) REVERT: Z 216 MET cc_start: 0.8420 (mtm) cc_final: 0.7948 (mtm) outliers start: 58 outliers final: 11 residues processed: 378 average time/residue: 0.5697 time to fit residues: 229.9341 Evaluate side-chains 306 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 67 LYS Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 153 ASN V 247 HIS W 83 HIS X 247 HIS Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.104160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091206 restraints weight = 20473.328| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.28 r_work: 0.3317 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 9920 Z= 0.351 Angle : 0.712 7.740 13425 Z= 0.368 Chirality : 0.048 0.321 1430 Planarity : 0.006 0.063 1705 Dihedral : 5.199 45.776 1305 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 5.51 % Allowed : 22.32 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1155 helix: 0.35 (0.22), residues: 540 sheet: -0.32 (0.26), residues: 330 loop : -0.65 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 165 TYR 0.024 0.002 TYR Y 157 PHE 0.021 0.002 PHE V 143 TRP 0.010 0.002 TRP Y 197 HIS 0.005 0.001 HIS W 58 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 9920) covalent geometry : angle 0.71236 (13425) hydrogen bonds : bond 0.04566 ( 564) hydrogen bonds : angle 5.93174 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 285 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 147 ASP cc_start: 0.8100 (m-30) cc_final: 0.7874 (m-30) REVERT: W 30 ASN cc_start: 0.8298 (t0) cc_final: 0.8041 (t0) REVERT: W 102 TYR cc_start: 0.8436 (t80) cc_final: 0.8118 (t80) REVERT: W 105 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8709 (p) REVERT: W 129 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8152 (ttp-110) REVERT: W 165 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7480 (mtm110) REVERT: W 173 MET cc_start: 0.8069 (mmp) cc_final: 0.7830 (mmp) REVERT: W 207 LEU cc_start: 0.8877 (tp) cc_final: 0.8552 (tm) REVERT: X 196 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7976 (mt-10) REVERT: Y 174 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7124 (p) REVERT: Z 161 MET cc_start: 0.7289 (mpt) cc_final: 0.7002 (mpt) REVERT: Z 165 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7149 (mtt-85) REVERT: Z 193 ASP cc_start: 0.8717 (t70) cc_final: 0.8476 (t0) REVERT: Z 207 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (tm) outliers start: 57 outliers final: 28 residues processed: 318 average time/residue: 0.5598 time to fit residues: 190.0131 Evaluate side-chains 292 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 211 LYS Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 207 LEU Chi-restraints excluded: chain Z residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 171 HIS V 241 ASN V 247 HIS X 55 GLN X 171 HIS X 241 ASN Y 171 HIS Z 30 ASN Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094890 restraints weight = 20732.189| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.32 r_work: 0.3382 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9920 Z= 0.150 Angle : 0.600 7.714 13425 Z= 0.306 Chirality : 0.044 0.226 1430 Planarity : 0.005 0.050 1705 Dihedral : 4.647 19.590 1301 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 4.73 % Allowed : 22.90 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.24), residues: 1155 helix: 0.54 (0.22), residues: 545 sheet: -0.37 (0.26), residues: 330 loop : -0.19 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 165 TYR 0.018 0.002 TYR Y 157 PHE 0.019 0.002 PHE W 232 TRP 0.013 0.001 TRP X 156 HIS 0.005 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9920) covalent geometry : angle 0.60034 (13425) hydrogen bonds : bond 0.03672 ( 564) hydrogen bonds : angle 5.58996 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: V 67 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8361 (mtmm) REVERT: V 217 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8524 (ttm170) REVERT: W 30 ASN cc_start: 0.8233 (t0) cc_final: 0.7954 (t0) REVERT: W 102 TYR cc_start: 0.8308 (t80) cc_final: 0.7998 (t80) REVERT: W 140 TYR cc_start: 0.8981 (m-80) cc_final: 0.8673 (m-80) REVERT: W 165 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7520 (mtm110) REVERT: W 173 MET cc_start: 0.8078 (mmp) cc_final: 0.7862 (mmp) REVERT: W 193 ASP cc_start: 0.8533 (t0) cc_final: 0.8274 (m-30) REVERT: W 207 LEU cc_start: 0.8758 (tp) cc_final: 0.8369 (tm) REVERT: W 210 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8625 (tptp) REVERT: X 196 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7990 (mt-10) REVERT: Y 165 ARG cc_start: 0.7487 (ttm170) cc_final: 0.6771 (mtm-85) REVERT: Y 174 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7161 (p) REVERT: Y 196 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7449 (mt-10) REVERT: Z 30 ASN cc_start: 0.8214 (t0) cc_final: 0.7901 (t0) REVERT: Z 161 MET cc_start: 0.7300 (mpt) cc_final: 0.7033 (mpt) REVERT: Z 165 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.7140 (mtm110) REVERT: Z 193 ASP cc_start: 0.8581 (t70) cc_final: 0.8342 (t0) REVERT: Z 196 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8052 (mt-10) REVERT: Z 220 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7268 (tm-30) outliers start: 49 outliers final: 22 residues processed: 341 average time/residue: 0.5533 time to fit residues: 201.7422 Evaluate side-chains 314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 67 LYS Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 220 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.0050 chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 151 GLN V 241 ASN V 247 HIS Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096699 restraints weight = 20592.213| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.28 r_work: 0.3419 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9920 Z= 0.132 Angle : 0.590 8.362 13425 Z= 0.298 Chirality : 0.043 0.197 1430 Planarity : 0.005 0.052 1705 Dihedral : 4.446 18.886 1300 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 5.12 % Allowed : 24.83 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1155 helix: 0.60 (0.22), residues: 540 sheet: -0.26 (0.26), residues: 330 loop : 0.07 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 165 TYR 0.012 0.001 TYR W 157 PHE 0.015 0.001 PHE W 17 TRP 0.014 0.001 TRP X 156 HIS 0.006 0.001 HIS W 15 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9920) covalent geometry : angle 0.59039 (13425) hydrogen bonds : bond 0.03465 ( 564) hydrogen bonds : angle 5.42918 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 129 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7592 (ttp80) REVERT: V 217 ARG cc_start: 0.8792 (ttm170) cc_final: 0.8530 (ttm170) REVERT: W 30 ASN cc_start: 0.8224 (t0) cc_final: 0.7964 (t0) REVERT: W 102 TYR cc_start: 0.8316 (t80) cc_final: 0.7985 (t80) REVERT: W 173 MET cc_start: 0.8087 (mmp) cc_final: 0.7876 (mmp) REVERT: W 196 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7869 (mt-10) REVERT: W 207 LEU cc_start: 0.8761 (tp) cc_final: 0.8326 (tm) REVERT: X 104 TYR cc_start: 0.8515 (t80) cc_final: 0.8208 (t80) REVERT: X 157 TYR cc_start: 0.7744 (m-80) cc_final: 0.7354 (m-80) REVERT: X 196 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7558 (mt-10) REVERT: Y 161 MET cc_start: 0.7235 (mpt) cc_final: 0.6912 (mpt) REVERT: Y 165 ARG cc_start: 0.7567 (ttm170) cc_final: 0.6867 (mtm-85) REVERT: Y 174 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7034 (p) REVERT: Z 161 MET cc_start: 0.7190 (mpt) cc_final: 0.6925 (mpt) REVERT: Z 193 ASP cc_start: 0.8543 (t70) cc_final: 0.8327 (t0) outliers start: 53 outliers final: 26 residues processed: 335 average time/residue: 0.5692 time to fit residues: 203.2849 Evaluate side-chains 316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 146 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 247 HIS X 247 HIS Z 30 ASN Z 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095936 restraints weight = 20775.018| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.30 r_work: 0.3406 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9920 Z= 0.153 Angle : 0.616 10.431 13425 Z= 0.307 Chirality : 0.043 0.229 1430 Planarity : 0.005 0.056 1705 Dihedral : 4.416 18.479 1300 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 5.60 % Allowed : 25.80 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1155 helix: 0.71 (0.22), residues: 540 sheet: -0.19 (0.26), residues: 310 loop : 0.37 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 165 TYR 0.011 0.001 TYR X 102 PHE 0.018 0.002 PHE Z 195 TRP 0.010 0.001 TRP X 156 HIS 0.004 0.001 HIS Y 15 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9920) covalent geometry : angle 0.61602 (13425) hydrogen bonds : bond 0.03511 ( 564) hydrogen bonds : angle 5.47921 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 129 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7519 (ttp80) REVERT: V 159 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7701 (mp) REVERT: W 30 ASN cc_start: 0.8262 (t0) cc_final: 0.8020 (t0) REVERT: W 105 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8175 (p) REVERT: W 140 TYR cc_start: 0.8928 (m-80) cc_final: 0.8695 (m-80) REVERT: W 173 MET cc_start: 0.8093 (mmp) cc_final: 0.7865 (mmp) REVERT: W 207 LEU cc_start: 0.8755 (tp) cc_final: 0.8312 (tm) REVERT: X 196 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7957 (mt-10) REVERT: Y 129 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7598 (ttp80) REVERT: Y 147 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7676 (t0) REVERT: Y 161 MET cc_start: 0.7263 (mpt) cc_final: 0.6900 (mpt) REVERT: Y 165 ARG cc_start: 0.7532 (ttm170) cc_final: 0.6985 (mtm110) REVERT: Y 174 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7013 (p) REVERT: Y 196 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7797 (mt-10) REVERT: Z 193 ASP cc_start: 0.8518 (t70) cc_final: 0.8308 (t0) REVERT: Z 196 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8037 (mt-10) outliers start: 58 outliers final: 35 residues processed: 336 average time/residue: 0.5667 time to fit residues: 203.2499 Evaluate side-chains 316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 147 ASP Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 241 ASN X 247 HIS Z 30 ASN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096159 restraints weight = 20663.744| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.29 r_work: 0.3412 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9920 Z= 0.163 Angle : 0.632 10.103 13425 Z= 0.314 Chirality : 0.043 0.197 1430 Planarity : 0.005 0.049 1705 Dihedral : 4.436 18.296 1300 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 5.80 % Allowed : 26.57 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1155 helix: 0.68 (0.22), residues: 540 sheet: -0.26 (0.26), residues: 310 loop : 0.42 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 165 TYR 0.020 0.002 TYR V 144 PHE 0.017 0.001 PHE W 202 TRP 0.010 0.001 TRP X 156 HIS 0.004 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9920) covalent geometry : angle 0.63171 (13425) hydrogen bonds : bond 0.03529 ( 564) hydrogen bonds : angle 5.54108 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8295 (mmm160) cc_final: 0.8089 (mmt-90) REVERT: V 159 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7761 (mp) REVERT: W 30 ASN cc_start: 0.8298 (t0) cc_final: 0.8068 (t0) REVERT: W 102 TYR cc_start: 0.8360 (t80) cc_final: 0.8048 (t80) REVERT: W 105 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8450 (p) REVERT: W 140 TYR cc_start: 0.8941 (m-80) cc_final: 0.8736 (m-80) REVERT: W 173 MET cc_start: 0.8103 (mmp) cc_final: 0.7864 (mmp) REVERT: W 207 LEU cc_start: 0.8757 (tp) cc_final: 0.8549 (tp) REVERT: X 129 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.7846 (mmm-85) REVERT: Y 129 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7552 (ttp80) REVERT: Y 161 MET cc_start: 0.7225 (mpt) cc_final: 0.6877 (mpt) REVERT: Y 165 ARG cc_start: 0.7550 (ttm170) cc_final: 0.6994 (mtm110) REVERT: Y 174 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.6996 (p) REVERT: Y 196 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7794 (mt-10) REVERT: Z 30 ASN cc_start: 0.8321 (t0) cc_final: 0.8043 (t0) REVERT: Z 176 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7774 (ptp90) REVERT: Z 193 ASP cc_start: 0.8536 (t70) cc_final: 0.8329 (t0) REVERT: Z 220 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7374 (tm-30) outliers start: 60 outliers final: 35 residues processed: 321 average time/residue: 0.5358 time to fit residues: 184.1185 Evaluate side-chains 316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 220 GLU Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.0010 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 241 ASN X 247 HIS Z 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097914 restraints weight = 20995.263| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.21 r_work: 0.3435 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9920 Z= 0.139 Angle : 0.626 9.459 13425 Z= 0.312 Chirality : 0.043 0.194 1430 Planarity : 0.005 0.049 1705 Dihedral : 4.368 18.950 1300 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 4.64 % Allowed : 28.12 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1155 helix: 0.69 (0.22), residues: 540 sheet: -0.21 (0.26), residues: 310 loop : 0.46 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 165 TYR 0.013 0.001 TYR X 102 PHE 0.017 0.001 PHE W 202 TRP 0.014 0.001 TRP X 156 HIS 0.004 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9920) covalent geometry : angle 0.62564 (13425) hydrogen bonds : bond 0.03453 ( 564) hydrogen bonds : angle 5.44794 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8043 (mmt-90) REVERT: V 129 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7116 (mmm-85) REVERT: V 159 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7771 (mp) REVERT: W 30 ASN cc_start: 0.8262 (t0) cc_final: 0.8031 (t0) REVERT: W 102 TYR cc_start: 0.8330 (t80) cc_final: 0.8020 (t80) REVERT: W 105 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8349 (p) REVERT: W 137 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8420 (mmtm) REVERT: W 140 TYR cc_start: 0.8873 (m-80) cc_final: 0.8645 (m-80) REVERT: W 173 MET cc_start: 0.8101 (mmp) cc_final: 0.7749 (mmp) REVERT: W 207 LEU cc_start: 0.8716 (tp) cc_final: 0.8278 (tm) REVERT: W 210 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8296 (tptm) REVERT: X 104 TYR cc_start: 0.8464 (t80) cc_final: 0.8238 (t80) REVERT: X 128 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.7976 (mmm160) REVERT: Y 161 MET cc_start: 0.7190 (mpt) cc_final: 0.6839 (mpt) REVERT: Y 165 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7161 (mtm110) REVERT: Y 174 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.6958 (p) REVERT: Y 176 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7804 (ptm160) REVERT: Z 176 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7734 (ptp90) outliers start: 48 outliers final: 30 residues processed: 315 average time/residue: 0.5516 time to fit residues: 185.4760 Evaluate side-chains 304 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 205 ASP Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 151 GLN X 241 ASN X 247 HIS Z 15 HIS Z 30 ASN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096433 restraints weight = 20659.965| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.31 r_work: 0.3411 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9920 Z= 0.175 Angle : 0.682 9.556 13425 Z= 0.337 Chirality : 0.045 0.305 1430 Planarity : 0.005 0.054 1705 Dihedral : 4.472 22.019 1300 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 4.35 % Allowed : 29.37 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1155 helix: 0.73 (0.22), residues: 545 sheet: -0.27 (0.26), residues: 310 loop : 0.45 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 165 TYR 0.016 0.002 TYR W 144 PHE 0.019 0.002 PHE Z 17 TRP 0.023 0.001 TRP V 197 HIS 0.004 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9920) covalent geometry : angle 0.68193 (13425) hydrogen bonds : bond 0.03569 ( 564) hydrogen bonds : angle 5.57109 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8226 (mmm160) cc_final: 0.8001 (mmt-90) REVERT: V 129 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7626 (ttp80) REVERT: V 159 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7759 (mp) REVERT: V 193 ASP cc_start: 0.8527 (t70) cc_final: 0.8223 (m-30) REVERT: W 30 ASN cc_start: 0.8234 (t0) cc_final: 0.8013 (t0) REVERT: W 102 TYR cc_start: 0.8302 (t80) cc_final: 0.8003 (t80) REVERT: W 105 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8315 (p) REVERT: W 137 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8472 (mmtm) REVERT: W 210 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8311 (tptm) REVERT: X 128 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.7948 (mmm160) REVERT: X 129 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.7769 (mmm-85) REVERT: X 146 MET cc_start: 0.8984 (ptp) cc_final: 0.8772 (ptt) REVERT: Y 158 MET cc_start: 0.7793 (mmm) cc_final: 0.7389 (mmm) REVERT: Y 161 MET cc_start: 0.7190 (mpt) cc_final: 0.6879 (mpt) REVERT: Y 165 ARG cc_start: 0.7599 (ttm170) cc_final: 0.6930 (mtm-85) REVERT: Y 174 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.6878 (p) REVERT: Y 176 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7821 (ptm160) REVERT: Z 30 ASN cc_start: 0.8274 (t0) cc_final: 0.8003 (t0) REVERT: Z 176 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7729 (ptp90) outliers start: 45 outliers final: 29 residues processed: 306 average time/residue: 0.5699 time to fit residues: 186.2019 Evaluate side-chains 296 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 83 HIS X 241 ASN Z 15 HIS Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095356 restraints weight = 20587.430| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.29 r_work: 0.3391 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9920 Z= 0.217 Angle : 0.723 10.258 13425 Z= 0.359 Chirality : 0.046 0.283 1430 Planarity : 0.006 0.058 1705 Dihedral : 4.621 22.924 1300 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 3.96 % Allowed : 30.43 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1155 helix: 0.66 (0.22), residues: 545 sheet: -0.43 (0.26), residues: 310 loop : 0.48 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 165 TYR 0.015 0.002 TYR W 104 PHE 0.018 0.002 PHE Z 17 TRP 0.028 0.001 TRP W 197 HIS 0.005 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 9920) covalent geometry : angle 0.72289 (13425) hydrogen bonds : bond 0.03755 ( 564) hydrogen bonds : angle 5.73460 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8261 (mmm160) cc_final: 0.8020 (mmt-90) REVERT: V 129 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7319 (mmm-85) REVERT: V 159 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7730 (mp) REVERT: W 30 ASN cc_start: 0.8235 (t0) cc_final: 0.8007 (t0) REVERT: W 102 TYR cc_start: 0.8292 (t80) cc_final: 0.7995 (t80) REVERT: W 105 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8366 (p) REVERT: W 176 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7031 (ptp90) REVERT: W 210 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8305 (tptm) REVERT: X 128 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.7961 (mmm160) REVERT: X 129 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7740 (mmm-85) REVERT: X 146 MET cc_start: 0.9030 (ptp) cc_final: 0.8806 (ptt) REVERT: Y 129 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7308 (mmm-85) REVERT: Y 147 ASP cc_start: 0.8386 (t0) cc_final: 0.7830 (t70) REVERT: Y 174 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.6906 (p) REVERT: Z 176 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7721 (ptp90) outliers start: 41 outliers final: 30 residues processed: 300 average time/residue: 0.5610 time to fit residues: 179.5349 Evaluate side-chains 304 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain V residue 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 205 ASP Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 55 GLN X 241 ASN Z 30 ASN Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095940 restraints weight = 20746.242| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.30 r_work: 0.3403 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9920 Z= 0.194 Angle : 0.729 10.623 13425 Z= 0.361 Chirality : 0.046 0.271 1430 Planarity : 0.006 0.056 1705 Dihedral : 4.647 22.764 1300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 3.57 % Allowed : 31.01 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.24), residues: 1155 helix: 0.59 (0.22), residues: 545 sheet: -0.55 (0.26), residues: 310 loop : 0.47 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Z 165 TYR 0.023 0.002 TYR V 144 PHE 0.020 0.002 PHE Z 17 TRP 0.027 0.001 TRP W 197 HIS 0.005 0.001 HIS Z 247 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9920) covalent geometry : angle 0.72942 (13425) hydrogen bonds : bond 0.03698 ( 564) hydrogen bonds : angle 5.76486 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4580.60 seconds wall clock time: 78 minutes 33.86 seconds (4713.86 seconds total)