Starting phenix.real_space_refine on Fri Feb 14 01:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_21376.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_21376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_21376.map" model { file = "/net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_21376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vsc_21376/02_2025/6vsc_21376.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.03, per 1000 atoms: 0.62 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.24 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: 3.13 Time building geometry restraints manager: 2.66 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: 0.02 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: 0.710 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- 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= 0.903 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 : 16.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (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 TRP 0.047 0.012 TRP W 25 HIS 0.018 0.007 HIS W 58 PHE 0.088 0.016 PHE Z 225 TYR 0.053 0.011 TYR X 140 ARG 0.030 0.005 ARG Y 129 *********************** 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 : 1.185 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: 0.6810 (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: 0.8024 (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: 0.8386 (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: 0.7885 (mp-120) REVERT: W 165 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8036 (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: 0.8917 (t0) REVERT: X 33 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8703 (mtm110) REVERT: X 34 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8758 (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: 0.8588 (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: 0.8155 (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: 0.7038 (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: 0.7656 (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: 12 residues processed: 405 average time/residue: 1.3937 time to fit residues: 599.2248 Evaluate side-chains 284 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Y 247 HIS Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093793 restraints weight = 19223.447| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.20 r_work: 0.3320 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9920 Z= 0.252 Angle : 0.659 8.201 13425 Z= 0.346 Chirality : 0.044 0.180 1430 Planarity : 0.005 0.040 1705 Dihedral : 7.797 59.069 1369 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 5.41 % Allowed : 21.26 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1155 helix: -0.02 (0.21), residues: 535 sheet: -0.44 (0.26), residues: 365 loop : -0.80 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Z 156 HIS 0.004 0.001 HIS Z 247 PHE 0.020 0.002 PHE Z 225 TYR 0.020 0.002 TYR Y 157 ARG 0.006 0.001 ARG V 149 *********************** 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 397 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 147 ASP cc_start: 0.8231 (m-30) cc_final: 0.7976 (m-30) REVERT: V 153 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6652 (p0) REVERT: V 169 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7287 (ttp-170) REVERT: V 216 MET cc_start: 0.8071 (mtm) cc_final: 0.7732 (mtp) REVERT: W 30 ASN cc_start: 0.8272 (t0) cc_final: 0.7962 (t0) REVERT: W 102 TYR cc_start: 0.8275 (t80) cc_final: 0.7979 (t80) REVERT: W 129 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8142 (ttp-110) REVERT: W 165 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7437 (mtm110) REVERT: X 85 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9104 (mp) REVERT: X 151 GLN cc_start: 0.8945 (tp40) cc_final: 0.8698 (tt0) REVERT: X 196 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8000 (mt-10) REVERT: X 210 LYS cc_start: 0.9230 (tmmt) cc_final: 0.8995 (tttm) REVERT: X 215 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8431 (tp30) REVERT: X 216 MET cc_start: 0.8036 (mtm) cc_final: 0.7755 (mtp) REVERT: Y 129 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7733 (ttm-80) REVERT: Y 147 ASP cc_start: 0.8255 (m-30) cc_final: 0.7756 (m-30) REVERT: Y 196 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7249 (mt-10) REVERT: Y 216 MET cc_start: 0.8262 (mtm) cc_final: 0.7754 (mtp) REVERT: Z 129 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8263 (ttp-110) REVERT: Z 147 ASP cc_start: 0.8011 (m-30) cc_final: 0.7733 (m-30) REVERT: Z 165 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.7060 (mtm110) REVERT: Z 193 ASP cc_start: 0.8360 (t0) cc_final: 0.8062 (t0) REVERT: Z 196 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7657 (mt-10) REVERT: Z 216 MET cc_start: 0.8425 (mtm) cc_final: 0.7947 (mtm) outliers start: 56 outliers final: 12 residues processed: 376 average time/residue: 1.2237 time to fit residues: 491.7410 Evaluate side-chains 309 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 153 ASN 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 X residue 85 ILE Chi-restraints excluded: chain X residue 215 GLU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 67 LYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 239 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 X 247 HIS Z 30 ASN 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 = 0.3685 r_free = 0.3685 target = 0.107023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094168 restraints weight = 20380.905| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.33 r_work: 0.3366 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3830 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= 0.260 Angle : 0.627 7.380 13425 Z= 0.320 Chirality : 0.044 0.311 1430 Planarity : 0.005 0.060 1705 Dihedral : 5.320 57.088 1311 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 5.31 % Allowed : 22.13 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1155 helix: 0.49 (0.22), residues: 540 sheet: -0.22 (0.26), residues: 330 loop : -0.45 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 156 HIS 0.004 0.001 HIS Z 247 PHE 0.019 0.002 PHE W 232 TYR 0.020 0.002 TYR Y 157 ARG 0.008 0.001 ARG V 165 *********************** 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 368 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 196 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8016 (mt-10) REVERT: W 30 ASN cc_start: 0.8241 (t0) cc_final: 0.7967 (t0) REVERT: W 102 TYR cc_start: 0.8405 (t80) cc_final: 0.8119 (t80) REVERT: W 105 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8553 (p) REVERT: W 129 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8121 (ttp-110) REVERT: W 165 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7510 (mtm110) REVERT: W 207 LEU cc_start: 0.8783 (tp) cc_final: 0.8560 (tm) REVERT: W 210 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8402 (tptm) REVERT: X 85 ILE cc_start: 0.9304 (mm) cc_final: 0.9084 (mp) REVERT: X 102 TYR cc_start: 0.8514 (t80) cc_final: 0.8275 (t80) REVERT: X 193 ASP cc_start: 0.8605 (t0) cc_final: 0.8133 (t0) REVERT: X 196 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7974 (mt-10) REVERT: Y 165 ARG cc_start: 0.7506 (ttm170) cc_final: 0.6895 (mtm-85) REVERT: Y 174 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7130 (p) REVERT: Y 196 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7764 (mt-10) REVERT: Z 30 ASN cc_start: 0.8161 (t0) cc_final: 0.7904 (t0) REVERT: Z 165 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7126 (mtm110) outliers start: 55 outliers final: 26 residues processed: 345 average time/residue: 1.1989 time to fit residues: 442.5571 Evaluate side-chains 308 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU 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 190 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 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 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 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 Y residue 212 LEU Chi-restraints excluded: chain Z residue 37 ILE 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 239 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 171 HIS V 241 ASN V 247 HIS X 171 HIS X 241 ASN X 247 HIS Y 171 HIS 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 = 0.3699 r_free = 0.3699 target = 0.107648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094988 restraints weight = 20120.330| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.29 r_work: 0.3392 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9920 Z= 0.233 Angle : 0.617 7.929 13425 Z= 0.311 Chirality : 0.043 0.232 1430 Planarity : 0.005 0.051 1705 Dihedral : 4.614 20.807 1300 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Rotamer: Outliers : 4.64 % Allowed : 23.09 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1155 helix: 0.64 (0.22), residues: 545 sheet: -0.30 (0.26), residues: 330 loop : -0.13 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 156 HIS 0.004 0.001 HIS Z 247 PHE 0.017 0.002 PHE W 232 TYR 0.014 0.002 TYR V 157 ARG 0.008 0.001 ARG V 165 *********************** 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 352 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 109 GLU cc_start: 0.7525 (pt0) cc_final: 0.7188 (pt0) REVERT: W 30 ASN cc_start: 0.8228 (t0) cc_final: 0.7936 (t0) REVERT: W 165 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7439 (mtm110) REVERT: W 176 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7396 (ptp90) REVERT: W 193 ASP cc_start: 0.8581 (t0) cc_final: 0.8360 (m-30) REVERT: W 207 LEU cc_start: 0.8764 (tp) cc_final: 0.8423 (tm) REVERT: W 210 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8298 (tptm) REVERT: X 102 TYR cc_start: 0.8467 (t80) cc_final: 0.8225 (t80) REVERT: X 130 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7936 (ttt180) REVERT: X 196 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8001 (mt-10) REVERT: Y 147 ASP cc_start: 0.8046 (m-30) cc_final: 0.7767 (m-30) REVERT: Y 165 ARG cc_start: 0.7606 (ttm170) cc_final: 0.6940 (mtm-85) REVERT: Y 196 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7214 (mt-10) REVERT: Z 165 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7205 (mtm110) REVERT: Z 196 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7990 (mt-10) REVERT: Z 220 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7339 (tm-30) outliers start: 48 outliers final: 26 residues processed: 332 average time/residue: 1.1973 time to fit residues: 425.5822 Evaluate side-chains 315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS 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 64 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 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 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU 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 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 212 LEU 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 72 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 0.0040 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- 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 W 55 GLN W 83 HIS X 241 ASN X 247 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 = 0.3677 r_free = 0.3677 target = 0.106732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094034 restraints weight = 20225.464| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.27 r_work: 0.3359 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9920 Z= 0.324 Angle : 0.642 8.293 13425 Z= 0.325 Chirality : 0.044 0.281 1430 Planarity : 0.005 0.048 1705 Dihedral : 4.619 20.697 1300 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 5.51 % Allowed : 23.96 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1155 helix: 0.58 (0.22), residues: 540 sheet: -0.33 (0.26), residues: 310 loop : 0.18 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 197 HIS 0.003 0.001 HIS Z 247 PHE 0.016 0.002 PHE V 143 TYR 0.016 0.002 TYR V 157 ARG 0.009 0.001 ARG V 165 *********************** 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 347 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 109 GLU cc_start: 0.7590 (pt0) cc_final: 0.7297 (pt0) REVERT: W 30 ASN cc_start: 0.8248 (t0) cc_final: 0.7966 (t0) REVERT: W 102 TYR cc_start: 0.8384 (t80) cc_final: 0.8064 (t80) REVERT: W 105 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8567 (p) REVERT: W 140 TYR cc_start: 0.8985 (m-80) cc_final: 0.8760 (m-80) REVERT: W 165 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7467 (mtm110) REVERT: W 176 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7525 (ptp90) REVERT: W 207 LEU cc_start: 0.8814 (tp) cc_final: 0.8366 (tm) REVERT: W 210 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8333 (tptm) REVERT: X 196 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7999 (mt-10) REVERT: Y 147 ASP cc_start: 0.8058 (m-30) cc_final: 0.7770 (m-30) REVERT: Y 165 ARG cc_start: 0.7584 (ttm170) cc_final: 0.6931 (mtm-85) REVERT: Y 174 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7132 (p) REVERT: Y 196 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7346 (mt-10) REVERT: Z 30 ASN cc_start: 0.8297 (t0) cc_final: 0.8036 (t0) REVERT: Z 165 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.7096 (mtt-85) REVERT: Z 196 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8096 (mt-10) REVERT: Z 220 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7400 (tm-30) outliers start: 57 outliers final: 33 residues processed: 322 average time/residue: 1.2153 time to fit residues: 419.3624 Evaluate side-chains 316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU 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 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 210 LYS Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 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 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 212 LEU Chi-restraints excluded: chain Z residue 220 GLU Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 247 HIS Z 55 GLN 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 = 0.3661 r_free = 0.3661 target = 0.105193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.092401 restraints weight = 20510.539| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.28 r_work: 0.3345 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9920 Z= 0.396 Angle : 0.684 10.270 13425 Z= 0.344 Chirality : 0.044 0.209 1430 Planarity : 0.005 0.049 1705 Dihedral : 4.721 20.669 1300 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 6.18 % Allowed : 24.44 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1155 helix: 0.53 (0.22), residues: 545 sheet: -0.50 (0.26), residues: 310 loop : 0.17 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 197 HIS 0.005 0.001 HIS Y 15 PHE 0.018 0.002 PHE V 143 TYR 0.019 0.002 TYR V 157 ARG 0.011 0.001 ARG V 165 *********************** 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 344 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 280 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 109 GLU cc_start: 0.7565 (pt0) cc_final: 0.7202 (pt0) REVERT: W 30 ASN cc_start: 0.8240 (t0) cc_final: 0.7991 (t0) REVERT: W 102 TYR cc_start: 0.8380 (t80) cc_final: 0.8053 (t80) REVERT: W 105 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8639 (p) REVERT: W 165 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7522 (mtm110) REVERT: X 176 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7517 (ptp90) REVERT: X 196 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7970 (mt-10) REVERT: Y 174 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7129 (p) REVERT: Z 165 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7095 (mtm110) REVERT: Z 196 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8109 (mt-10) REVERT: Z 220 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7369 (tm-30) outliers start: 64 outliers final: 39 residues processed: 319 average time/residue: 1.2153 time to fit residues: 414.6855 Evaluate side-chains 314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU 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 190 VAL Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 14 LEU 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 210 LYS Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 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 192 LEU Chi-restraints excluded: chain Y residue 211 LYS 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 184 GLN Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 211 LYS Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 241 ASN Z 30 ASN Z 55 GLN 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 = 0.3693 r_free = 0.3693 target = 0.107245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094528 restraints weight = 20697.869| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.30 r_work: 0.3383 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9920 Z= 0.252 Angle : 0.642 9.838 13425 Z= 0.323 Chirality : 0.044 0.219 1430 Planarity : 0.005 0.047 1705 Dihedral : 4.630 21.014 1300 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 5.80 % Allowed : 26.18 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1155 helix: 0.60 (0.22), residues: 545 sheet: -0.56 (0.26), residues: 310 loop : 0.23 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 197 HIS 0.004 0.001 HIS Z 247 PHE 0.013 0.002 PHE Z 195 TYR 0.015 0.002 TYR Y 157 ARG 0.011 0.001 ARG V 165 *********************** 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 352 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 218 PHE cc_start: 0.7590 (m-10) cc_final: 0.7387 (m-10) REVERT: W 30 ASN cc_start: 0.8229 (t0) cc_final: 0.7971 (t0) REVERT: W 102 TYR cc_start: 0.8330 (t80) cc_final: 0.8004 (t80) REVERT: W 105 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8521 (p) REVERT: W 165 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7476 (mtm110) REVERT: W 176 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7365 (ptp90) REVERT: W 196 GLU cc_start: 0.8249 (pt0) cc_final: 0.8030 (pt0) REVERT: W 207 LEU cc_start: 0.8793 (tp) cc_final: 0.8537 (tm) REVERT: W 210 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: X 196 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7905 (mt-10) REVERT: Y 129 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7526 (ttp80) REVERT: Y 161 MET cc_start: 0.7119 (mpt) cc_final: 0.6806 (mpt) REVERT: Y 165 ARG cc_start: 0.7654 (ttm170) cc_final: 0.6969 (mtm-85) REVERT: Y 174 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7136 (p) REVERT: Z 30 ASN cc_start: 0.8285 (t0) cc_final: 0.7995 (t0) REVERT: Z 165 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7118 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7793 (ptp90) REVERT: Z 196 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7955 (mt-10) REVERT: Z 220 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7323 (tm-30) outliers start: 60 outliers final: 43 residues processed: 332 average time/residue: 1.1697 time to fit residues: 416.7919 Evaluate side-chains 335 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU 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 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 14 LEU 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 153 ASN 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 210 LYS Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 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 192 LEU Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 212 LEU 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 211 LYS Chi-restraints excluded: chain Z residue 212 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 11 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 241 ASN V 247 HIS X 55 GLN X 241 ASN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095083 restraints weight = 20889.462| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.30 r_work: 0.3392 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9920 Z= 0.240 Angle : 0.663 9.516 13425 Z= 0.330 Chirality : 0.044 0.213 1430 Planarity : 0.005 0.050 1705 Dihedral : 4.608 20.659 1300 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 5.41 % Allowed : 28.12 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1155 helix: 0.54 (0.22), residues: 540 sheet: -0.69 (0.25), residues: 320 loop : 0.49 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 197 HIS 0.005 0.001 HIS Z 247 PHE 0.014 0.002 PHE Z 17 TYR 0.019 0.002 TYR V 144 ARG 0.011 0.001 ARG V 165 *********************** 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 346 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.8152 (mmt-90) REVERT: W 30 ASN cc_start: 0.8243 (t0) cc_final: 0.8002 (t0) REVERT: W 102 TYR cc_start: 0.8306 (t80) cc_final: 0.8019 (t80) REVERT: W 105 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8532 (p) REVERT: W 165 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7461 (mtm110) REVERT: W 176 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7257 (ptp90) REVERT: W 196 GLU cc_start: 0.8241 (pt0) cc_final: 0.8041 (pt0) REVERT: W 207 LEU cc_start: 0.8783 (tp) cc_final: 0.8399 (tm) REVERT: W 210 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8577 (tptp) REVERT: X 128 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7964 (mmt-90) REVERT: X 129 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7875 (mmm-85) REVERT: X 176 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7456 (ptp90) REVERT: Y 157 TYR cc_start: 0.7418 (m-80) cc_final: 0.7206 (m-80) REVERT: Y 161 MET cc_start: 0.7085 (mpt) cc_final: 0.6762 (mpt) REVERT: Y 165 ARG cc_start: 0.7648 (ttm170) cc_final: 0.6967 (mtm-85) REVERT: Y 174 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7028 (p) REVERT: Z 165 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7152 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8309 (mtp85) cc_final: 0.7786 (ptp90) REVERT: Z 196 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8068 (mt-10) REVERT: Z 210 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8972 (tmmt) REVERT: Z 220 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7302 (tm-30) outliers start: 56 outliers final: 39 residues processed: 327 average time/residue: 1.1755 time to fit residues: 412.7778 Evaluate side-chains 324 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 169 ARG Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 205 ASP 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 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 210 LYS Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 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 192 LEU Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 212 LEU 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 211 LYS Chi-restraints excluded: chain Z residue 220 GLU 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 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 Z 15 HIS Z 30 ASN 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 = 0.3706 r_free = 0.3706 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095771 restraints weight = 20640.610| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.30 r_work: 0.3394 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9920 Z= 0.244 Angle : 0.686 9.669 13425 Z= 0.341 Chirality : 0.044 0.208 1430 Planarity : 0.005 0.054 1705 Dihedral : 4.629 21.196 1300 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 4.54 % Allowed : 29.76 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1155 helix: 0.61 (0.22), residues: 545 sheet: -0.53 (0.26), residues: 310 loop : 0.33 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 197 HIS 0.005 0.001 HIS Z 247 PHE 0.018 0.002 PHE V 195 TYR 0.013 0.002 TYR W 144 ARG 0.012 0.001 ARG V 165 *********************** 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 331 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8417 (mmt-90) cc_final: 0.8168 (mmt-90) REVERT: W 30 ASN cc_start: 0.8240 (t0) cc_final: 0.8009 (t0) REVERT: W 45 ASP cc_start: 0.8436 (t0) cc_final: 0.8116 (m-30) REVERT: W 102 TYR cc_start: 0.8285 (t80) cc_final: 0.8001 (t80) REVERT: W 105 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8553 (p) REVERT: W 130 ARG cc_start: 0.7564 (ttt180) cc_final: 0.7275 (ttt180) REVERT: W 165 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7504 (mtm110) REVERT: W 176 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7246 (ptp90) REVERT: W 207 LEU cc_start: 0.8779 (tp) cc_final: 0.8412 (tm) REVERT: W 210 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8573 (tptp) REVERT: X 129 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7883 (mmm-85) REVERT: X 147 ASP cc_start: 0.8278 (m-30) cc_final: 0.8060 (m-30) REVERT: X 196 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7970 (pt0) REVERT: Y 105 VAL cc_start: 0.8937 (t) cc_final: 0.8580 (p) REVERT: Y 161 MET cc_start: 0.7125 (mpt) cc_final: 0.6803 (mpt) REVERT: Y 165 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6967 (mtm-85) REVERT: Y 174 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.6959 (p) REVERT: Z 30 ASN cc_start: 0.8312 (t0) cc_final: 0.8060 (t0) REVERT: Z 147 ASP cc_start: 0.7933 (m-30) cc_final: 0.7678 (m-30) REVERT: Z 165 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7131 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7860 (ptp90) REVERT: Z 196 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7969 (mt-10) REVERT: Z 220 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7280 (tm-30) outliers start: 47 outliers final: 35 residues processed: 315 average time/residue: 1.2112 time to fit residues: 412.1193 Evaluate side-chains 321 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 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 205 ASP Chi-restraints excluded: chain X residue 210 LYS Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 160 SER Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Y residue 212 LEU 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 220 GLU 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 101 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 184 GLN X 241 ASN Y 241 ASN Z 15 HIS 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 = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096404 restraints weight = 21134.154| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.24 r_work: 0.3407 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4622 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= 0.234 Angle : 0.692 10.107 13425 Z= 0.344 Chirality : 0.044 0.197 1430 Planarity : 0.005 0.055 1705 Dihedral : 4.617 20.922 1300 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 4.25 % Allowed : 30.43 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1155 helix: 0.63 (0.22), residues: 545 sheet: -0.56 (0.26), residues: 310 loop : 0.33 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 197 HIS 0.005 0.001 HIS Z 247 PHE 0.019 0.002 PHE Z 17 TYR 0.012 0.001 TYR X 102 ARG 0.013 0.001 ARG V 165 ********************** 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 336 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 128 ARG cc_start: 0.8417 (mmt-90) cc_final: 0.8180 (mmt-90) REVERT: V 195 PHE cc_start: 0.8323 (m-80) cc_final: 0.8012 (m-80) REVERT: W 30 ASN cc_start: 0.8230 (t0) cc_final: 0.7999 (t0) REVERT: W 45 ASP cc_start: 0.8397 (t0) cc_final: 0.8103 (m-30) REVERT: W 102 TYR cc_start: 0.8275 (t80) cc_final: 0.8007 (t80) REVERT: W 105 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8514 (p) REVERT: W 130 ARG cc_start: 0.7639 (ttt180) cc_final: 0.7363 (ttt180) REVERT: W 165 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7473 (mtm110) REVERT: W 176 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7267 (ptp90) REVERT: W 207 LEU cc_start: 0.8762 (tp) cc_final: 0.8387 (tm) REVERT: W 210 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8557 (tptp) REVERT: X 128 ARG cc_start: 0.8233 (mmm160) cc_final: 0.8008 (mmt-90) REVERT: X 129 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.7868 (mmm-85) REVERT: X 147 ASP cc_start: 0.8189 (m-30) cc_final: 0.7887 (m-30) REVERT: X 193 ASP cc_start: 0.8506 (t0) cc_final: 0.8132 (m-30) REVERT: X 196 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8022 (pt0) REVERT: X 207 LEU cc_start: 0.8796 (tp) cc_final: 0.8496 (tm) REVERT: Y 105 VAL cc_start: 0.8926 (t) cc_final: 0.8641 (p) REVERT: Y 129 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7459 (mmm-85) REVERT: Y 158 MET cc_start: 0.7764 (mmm) cc_final: 0.7273 (mmm) REVERT: Y 161 MET cc_start: 0.7089 (mpt) cc_final: 0.6773 (mpt) REVERT: Y 165 ARG cc_start: 0.7634 (ttm170) cc_final: 0.6961 (mtm-85) REVERT: Y 174 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.6945 (p) REVERT: Y 176 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7902 (ptm160) REVERT: Y 196 GLU cc_start: 0.8370 (pt0) cc_final: 0.8100 (pm20) REVERT: Z 129 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7595 (ttp80) REVERT: Z 130 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7154 (ttp80) REVERT: Z 147 ASP cc_start: 0.7943 (m-30) cc_final: 0.7694 (m-30) REVERT: Z 165 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.7070 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7838 (ptp90) REVERT: Z 196 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7956 (mt-10) outliers start: 44 outliers final: 33 residues processed: 325 average time/residue: 1.1753 time to fit residues: 409.6524 Evaluate side-chains 315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 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 210 LYS Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 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 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 62 optimal weight: 0.0170 chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 151 GLN V 241 ASN V 247 HIS X 241 ASN Z 15 HIS Z 30 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097609 restraints weight = 20735.636| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.24 r_work: 0.3423 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9920 Z= 0.216 Angle : 0.709 11.968 13425 Z= 0.348 Chirality : 0.044 0.194 1430 Planarity : 0.005 0.056 1705 Dihedral : 4.615 23.649 1300 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 3.77 % Allowed : 31.01 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1155 helix: 0.65 (0.22), residues: 545 sheet: -0.52 (0.26), residues: 310 loop : 0.39 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP W 197 HIS 0.006 0.001 HIS Z 247 PHE 0.022 0.002 PHE Z 17 TYR 0.023 0.001 TYR W 144 ARG 0.013 0.001 ARG V 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8898.92 seconds wall clock time: 157 minutes 31.06 seconds (9451.06 seconds total)