Starting phenix.real_space_refine on Sun Apr 27 22:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbv_36147/04_2025/8jbv_36147.cif" } resolution = 3.02 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= -0.002 sd= 0.090 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 26 5.16 5 C 4244 2.51 5 N 1114 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6624 Number of models: 1 Model: "" Number of chains: 4 Chain: "m" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain breaks: 1 Chain: "n" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1736 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "M" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain breaks: 1 Chain: "N" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1736 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.69 Number of scatterers: 6624 At special positions: 0 Unit cell: (81.525, 84.786, 133.701, 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 26 16.00 O 1240 8.00 N 1114 7.00 C 4244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS m 43 " - pdb=" SG CYS m 111 " distance=2.03 Simple disulfide: pdb=" SG CYS m 157 " - pdb=" SG CYS m 208 " distance=2.03 Simple disulfide: pdb=" SG CYS n 26 " - pdb=" SG CYS n 98 " distance=2.04 Simple disulfide: pdb=" SG CYS n 156 " - pdb=" SG CYS n 212 " distance=2.04 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 111 " distance=2.03 Simple disulfide: pdb=" SG CYS M 157 " - pdb=" SG CYS M 208 " distance=2.03 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 98 " distance=2.04 Simple disulfide: pdb=" SG CYS N 156 " - pdb=" SG CYS N 212 " distance=2.04 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: 1.47 Conformation dependent library (CDL) restraints added in 952.6 milliseconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 20 sheets defined 3.9% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'm' and resid 211 through 215 removed outlier: 4.341A pdb=" N ASN m 214 " --> pdb=" O GLN m 211 " (cutoff:3.500A) Processing helix chain 'n' and resid 89 through 93 removed outlier: 3.919A pdb=" N SER n 93 " --> pdb=" O GLU n 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 144 through 149 removed outlier: 3.833A pdb=" N LEU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 215 removed outlier: 4.341A pdb=" N ASN M 214 " --> pdb=" O GLN M 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 93 removed outlier: 3.919A pdb=" N SER N 93 " --> pdb=" O GLU N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.833A pdb=" N LEU N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'm' and resid 23 through 25 removed outlier: 3.581A pdb=" N VAL m 39 " --> pdb=" O ILE m 98 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER m 93 " --> pdb=" O LYS m 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR m 83 " --> pdb=" O SER m 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'm' and resid 30 through 34 removed outlier: 6.442A pdb=" N VAL m 31 " --> pdb=" O THR m 133 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU m 135 " --> pdb=" O VAL m 31 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET m 33 " --> pdb=" O GLU m 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA m 107 " --> pdb=" O VAL m 132 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE m 54 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG m 70 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP m 56 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'm' and resid 30 through 34 removed outlier: 6.442A pdb=" N VAL m 31 " --> pdb=" O THR m 133 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU m 135 " --> pdb=" O VAL m 31 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET m 33 " --> pdb=" O GLU m 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA m 107 " --> pdb=" O VAL m 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'm' and resid 146 through 150 removed outlier: 3.994A pdb=" N GLU m 161 " --> pdb=" O TYR m 192 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR m 192 " --> pdb=" O GLU m 161 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL m 195 " --> pdb=" O ALA m 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'n' and resid 13 through 14 removed outlier: 5.391A pdb=" N TRP n 101 " --> pdb=" O TYR n 35 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR n 35 " --> pdb=" O TRP n 101 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE n 36 " --> pdb=" O TYR n 52 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR n 52 " --> pdb=" O ILE n 36 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP n 38 " --> pdb=" O LEU n 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS n 59 " --> pdb=" O ASP n 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'n' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'n' and resid 152 through 153 removed outlier: 3.548A pdb=" N GLY n 152 " --> pdb=" O VAL n 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 156 through 159 removed outlier: 3.560A pdb=" N SER n 197 " --> pdb=" O CYS n 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'n' and resid 167 through 171 removed outlier: 3.554A pdb=" N GLN n 171 " --> pdb=" O ARG n 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.581A pdb=" N VAL M 39 " --> pdb=" O ILE M 98 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 93 " --> pdb=" O LYS M 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 30 through 34 removed outlier: 6.443A pdb=" N VAL M 31 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLU M 135 " --> pdb=" O VAL M 31 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET M 33 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 107 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE M 54 " --> pdb=" O ARG M 70 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG M 70 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP M 56 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 30 through 34 removed outlier: 6.443A pdb=" N VAL M 31 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLU M 135 " --> pdb=" O VAL M 31 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET M 33 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 107 " --> pdb=" O VAL M 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 146 through 150 removed outlier: 3.994A pdb=" N GLU M 161 " --> pdb=" O TYR M 192 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR M 192 " --> pdb=" O GLU M 161 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL M 195 " --> pdb=" O ALA M 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 13 through 14 removed outlier: 5.390A pdb=" N TRP N 101 " --> pdb=" O TYR N 35 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR N 35 " --> pdb=" O TRP N 101 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE N 36 " --> pdb=" O TYR N 52 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR N 52 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP N 38 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 59 " --> pdb=" O ASP N 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 21 through 25 Processing sheet with id=AB9, first strand: chain 'N' and resid 152 through 153 removed outlier: 3.548A pdb=" N GLY N 152 " --> pdb=" O VAL N 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.559A pdb=" N SER N 197 " --> pdb=" O CYS N 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 167 through 171 removed outlier: 3.553A pdb=" N GLN N 171 " --> pdb=" O ARG N 211 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1391 1.33 - 1.45: 1713 1.45 - 1.58: 3636 1.58 - 1.70: 4 1.70 - 1.83: 36 Bond restraints: 6780 Sorted by residual: bond pdb=" CB GLU m 104 " pdb=" CG GLU m 104 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.50e+00 bond pdb=" CB GLU M 104 " pdb=" CG GLU M 104 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.47e+00 bond pdb=" CB ASP n 164 " pdb=" CG ASP n 164 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.80e+00 bond pdb=" CB ASP N 164 " pdb=" CG ASP N 164 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.67e+00 bond pdb=" CB GLU n 209 " pdb=" CG GLU n 209 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.51e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 9052 3.33 - 6.67: 103 6.67 - 10.00: 18 10.00 - 13.34: 7 13.34 - 16.67: 4 Bond angle restraints: 9184 Sorted by residual: angle pdb=" CA GLU M 104 " pdb=" CB GLU M 104 " pdb=" CG GLU M 104 " ideal model delta sigma weight residual 114.10 129.38 -15.28 2.00e+00 2.50e-01 5.84e+01 angle pdb=" CA GLU m 104 " pdb=" CB GLU m 104 " pdb=" CG GLU m 104 " ideal model delta sigma weight residual 114.10 129.37 -15.27 2.00e+00 2.50e-01 5.83e+01 angle pdb=" C ASN n 219 " pdb=" CA ASN n 219 " pdb=" CB ASN n 219 " ideal model delta sigma weight residual 110.19 98.47 11.72 1.62e+00 3.81e-01 5.23e+01 angle pdb=" CA GLU N 209 " pdb=" CB GLU N 209 " pdb=" CG GLU N 209 " ideal model delta sigma weight residual 114.10 125.46 -11.36 2.00e+00 2.50e-01 3.23e+01 angle pdb=" CA GLU n 209 " pdb=" CB GLU n 209 " pdb=" CG GLU n 209 " ideal model delta sigma weight residual 114.10 125.46 -11.36 2.00e+00 2.50e-01 3.23e+01 ... (remaining 9179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3579 17.98 - 35.96: 299 35.96 - 53.94: 160 53.94 - 71.91: 58 71.91 - 89.89: 8 Dihedral angle restraints: 4104 sinusoidal: 1672 harmonic: 2432 Sorted by residual: dihedral pdb=" C ASN n 219 " pdb=" N ASN n 219 " pdb=" CA ASN n 219 " pdb=" CB ASN n 219 " ideal model delta harmonic sigma weight residual -122.60 -106.18 -16.42 0 2.50e+00 1.60e-01 4.31e+01 dihedral pdb=" CA THR N 146 " pdb=" C THR N 146 " pdb=" N LYS N 147 " pdb=" CA LYS N 147 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA THR n 146 " pdb=" C THR n 146 " pdb=" N LYS n 147 " pdb=" CA LYS n 147 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 813 0.073 - 0.146: 178 0.146 - 0.218: 29 0.218 - 0.291: 5 0.291 - 0.364: 3 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA ASN n 219 " pdb=" N ASN n 219 " pdb=" C ASN n 219 " pdb=" CB ASN n 219 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA PHE N 162 " pdb=" N PHE N 162 " pdb=" C PHE N 162 " pdb=" CB PHE N 162 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PHE n 162 " pdb=" N PHE n 162 " pdb=" C PHE n 162 " pdb=" CB PHE n 162 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1025 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN n 219 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN n 219 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN n 219 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS n 220 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO N 230 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO N 231 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO N 231 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO N 231 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO n 230 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO n 231 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO n 231 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO n 231 " 0.033 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1181 2.77 - 3.30: 5072 3.30 - 3.83: 10302 3.83 - 4.37: 11547 4.37 - 4.90: 21304 Nonbonded interactions: 49406 Sorted by model distance: nonbonded pdb=" OG1 THR n 153 " pdb=" OG1 THR n 200 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR N 153 " pdb=" OG1 THR N 200 " model vdw 2.235 3.040 nonbonded pdb=" O SER m 145 " pdb=" OG SER m 145 " model vdw 2.254 3.040 nonbonded pdb=" O SER M 145 " pdb=" OG SER M 145 " model vdw 2.254 3.040 nonbonded pdb=" O SER N 205 " pdb=" OG SER N 205 " model vdw 2.257 3.040 ... (remaining 49401 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: 0.03 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.008 0.076 6788 Z= 0.354 Angle : 1.123 16.669 9200 Z= 0.616 Chirality : 0.065 0.364 1028 Planarity : 0.008 0.063 1144 Dihedral : 18.530 89.893 2504 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 14.93 % Allowed : 7.73 % Favored : 77.33 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.26), residues: 808 helix: None (None), residues: 0 sheet: -1.27 (0.26), residues: 390 loop : -3.22 (0.22), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 38 HIS 0.004 0.001 HIS N 74 PHE 0.023 0.003 PHE n 162 TYR 0.022 0.003 TYR N 52 ARG 0.004 0.001 ARG m 36 Details of bonding type rmsd hydrogen bonds : bond 0.24296 ( 166) hydrogen bonds : angle 9.18024 ( 444) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.63900 ( 16) covalent geometry : bond 0.00816 ( 6780) covalent geometry : angle 1.12227 ( 9184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 149 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: m 30 SER cc_start: 0.7233 (OUTLIER) cc_final: 0.6890 (m) REVERT: m 32 SER cc_start: 0.6091 (OUTLIER) cc_final: 0.5785 (m) REVERT: m 46 GLU cc_start: 0.8186 (tt0) cc_final: 0.7975 (tt0) REVERT: m 53 TYR cc_start: 0.8034 (m-80) cc_final: 0.7782 (m-80) REVERT: m 125 ILE cc_start: 0.8249 (mt) cc_final: 0.7985 (mt) REVERT: m 205 SER cc_start: 0.6889 (OUTLIER) cc_final: 0.6642 (m) REVERT: M 65 MET cc_start: 0.7849 (mmt) cc_final: 0.7626 (tpp) REVERT: M 220 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6578 (m) REVERT: N 173 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.5206 (ptmt) REVERT: N 209 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6197 (tt0) outliers start: 112 outliers final: 17 residues processed: 237 average time/residue: 0.2033 time to fit residues: 61.3549 Evaluate side-chains 129 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 32 SER Chi-restraints excluded: chain m residue 133 THR Chi-restraints excluded: chain m residue 174 SER Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 205 SER Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain n residue 124 THR Chi-restraints excluded: chain n residue 205 SER Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 209 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 28 GLN m 42 ASN m 77 ASN m 102 GLN m 139 GLN m 193 ASN m 218 HIS n 32 ASN n 37 HIS n 169 HIS ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 42 ASN M 77 ASN M 102 GLN N 32 ASN N 37 HIS ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153417 restraints weight = 8411.125| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.96 r_work: 0.3625 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6788 Z= 0.155 Angle : 0.661 11.583 9200 Z= 0.344 Chirality : 0.049 0.162 1028 Planarity : 0.006 0.041 1144 Dihedral : 8.357 57.891 916 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.20 % Allowed : 16.80 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.27), residues: 808 helix: -4.57 (0.47), residues: 22 sheet: -1.02 (0.25), residues: 418 loop : -3.01 (0.25), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 79 HIS 0.002 0.001 HIS M 141 PHE 0.016 0.002 PHE N 162 TYR 0.013 0.002 TYR N 52 ARG 0.003 0.001 ARG n 49 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 166) hydrogen bonds : angle 6.25162 ( 444) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.20563 ( 16) covalent geometry : bond 0.00358 ( 6780) covalent geometry : angle 0.65921 ( 9184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: m 46 GLU cc_start: 0.8339 (tt0) cc_final: 0.8011 (tt0) REVERT: m 105 ASP cc_start: 0.7641 (m-30) cc_final: 0.7394 (m-30) REVERT: m 125 ILE cc_start: 0.8310 (mt) cc_final: 0.8096 (mt) REVERT: n 111 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.5393 (t80) REVERT: M 131 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6865 (ttm-80) REVERT: M 220 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7201 (m) outliers start: 39 outliers final: 29 residues processed: 142 average time/residue: 0.1984 time to fit residues: 37.5613 Evaluate side-chains 133 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 THR Chi-restraints excluded: chain m residue 149 MET Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 77 ARG Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 124 THR Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 181 SER Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 209 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 218 HIS n 32 ASN n 91 ASN ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.169594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145335 restraints weight = 8659.370| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.29 r_work: 0.3498 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6788 Z= 0.230 Angle : 0.733 14.454 9200 Z= 0.378 Chirality : 0.051 0.193 1028 Planarity : 0.006 0.055 1144 Dihedral : 7.050 56.759 897 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 5.33 % Allowed : 19.20 % Favored : 75.47 % 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: -2.78 (0.27), residues: 808 helix: -4.49 (0.48), residues: 22 sheet: -0.78 (0.26), residues: 402 loop : -2.90 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 49 HIS 0.004 0.001 HIS n 37 PHE 0.020 0.003 PHE N 196 TYR 0.017 0.002 TYR n 53 ARG 0.007 0.001 ARG N 49 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 166) hydrogen bonds : angle 6.09928 ( 444) SS BOND : bond 0.00383 ( 8) SS BOND : angle 1.29360 ( 16) covalent geometry : bond 0.00552 ( 6780) covalent geometry : angle 0.73185 ( 9184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 46 GLU cc_start: 0.8159 (tt0) cc_final: 0.7730 (tt0) REVERT: m 105 ASP cc_start: 0.7703 (m-30) cc_final: 0.7416 (m-30) REVERT: m 125 ILE cc_start: 0.8233 (mt) cc_final: 0.8014 (mt) REVERT: m 203 SER cc_start: 0.6046 (OUTLIER) cc_final: 0.5785 (p) REVERT: n 111 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5657 (t80) REVERT: M 131 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6859 (ttm-80) REVERT: N 43 GLU cc_start: 0.7741 (pp20) cc_final: 0.7495 (pp20) REVERT: N 147 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7157 (ptmm) outliers start: 40 outliers final: 29 residues processed: 147 average time/residue: 0.1967 time to fit residues: 38.2555 Evaluate side-chains 135 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 133 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 62 LEU Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 124 THR Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 181 SER Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 193 ASN m 218 HIS n 32 ASN n 91 ASN ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 77 ASN M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150292 restraints weight = 8754.487| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.42 r_work: 0.3546 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6788 Z= 0.108 Angle : 0.555 8.852 9200 Z= 0.291 Chirality : 0.046 0.189 1028 Planarity : 0.005 0.046 1144 Dihedral : 5.319 41.963 890 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.93 % Allowed : 19.20 % Favored : 75.87 % 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: -2.26 (0.28), residues: 808 helix: -4.06 (0.59), residues: 22 sheet: -0.34 (0.27), residues: 400 loop : -2.68 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP n 198 HIS 0.004 0.001 HIS n 169 PHE 0.014 0.001 PHE m 180 TYR 0.012 0.001 TYR n 53 ARG 0.003 0.000 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 166) hydrogen bonds : angle 5.60287 ( 444) SS BOND : bond 0.00216 ( 8) SS BOND : angle 1.05943 ( 16) covalent geometry : bond 0.00242 ( 6780) covalent geometry : angle 0.55417 ( 9184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: m 46 GLU cc_start: 0.8116 (tt0) cc_final: 0.7663 (tt0) REVERT: m 105 ASP cc_start: 0.7620 (m-30) cc_final: 0.7334 (m-30) REVERT: m 137 ARG cc_start: 0.5840 (ptt-90) cc_final: 0.5416 (ptt90) REVERT: n 111 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5197 (t80) REVERT: M 131 ARG cc_start: 0.7292 (ttm110) cc_final: 0.6884 (ttm-80) REVERT: M 170 ASN cc_start: 0.7702 (p0) cc_final: 0.7389 (p0) REVERT: N 43 GLU cc_start: 0.7659 (pp20) cc_final: 0.7368 (pp20) outliers start: 37 outliers final: 25 residues processed: 137 average time/residue: 0.2532 time to fit residues: 45.7703 Evaluate side-chains 126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 124 THR Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 6 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 218 HIS n 91 ASN n 182 GLN n 216 HIS M 22 GLN M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150699 restraints weight = 8667.915| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.23 r_work: 0.3576 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6788 Z= 0.096 Angle : 0.531 8.452 9200 Z= 0.277 Chirality : 0.045 0.197 1028 Planarity : 0.004 0.044 1144 Dihedral : 4.654 28.874 889 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.40 % Allowed : 19.73 % Favored : 75.87 % 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: -2.01 (0.29), residues: 808 helix: -3.60 (0.75), residues: 22 sheet: -0.12 (0.27), residues: 400 loop : -2.60 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 198 HIS 0.004 0.001 HIS n 169 PHE 0.010 0.001 PHE m 180 TYR 0.017 0.001 TYR m 192 ARG 0.004 0.000 ARG M 70 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 166) hydrogen bonds : angle 5.36120 ( 444) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.94517 ( 16) covalent geometry : bond 0.00213 ( 6780) covalent geometry : angle 0.52983 ( 9184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 33 MET cc_start: 0.7411 (tpp) cc_final: 0.7152 (tpp) REVERT: m 46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7691 (tt0) REVERT: n 87 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8303 (m-40) REVERT: n 111 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5409 (t80) REVERT: M 76 GLN cc_start: 0.6889 (pm20) cc_final: 0.6289 (tt0) REVERT: M 131 ARG cc_start: 0.7398 (ttm110) cc_final: 0.6998 (ttm-80) REVERT: M 161 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5895 (mt-10) REVERT: M 170 ASN cc_start: 0.7670 (p0) cc_final: 0.7393 (p0) REVERT: N 43 GLU cc_start: 0.7681 (pp20) cc_final: 0.7377 (pp20) outliers start: 33 outliers final: 25 residues processed: 136 average time/residue: 0.2169 time to fit residues: 40.2868 Evaluate side-chains 126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 124 THR Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 218 HIS n 32 ASN n 91 ASN n 182 GLN M 22 GLN M 120 ASN M 193 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151197 restraints weight = 8555.498| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.27 r_work: 0.3590 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6788 Z= 0.101 Angle : 0.533 8.203 9200 Z= 0.279 Chirality : 0.046 0.202 1028 Planarity : 0.004 0.042 1144 Dihedral : 4.235 23.282 886 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.33 % Allowed : 20.00 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.29), residues: 808 helix: -3.38 (0.81), residues: 22 sheet: 0.04 (0.28), residues: 400 loop : -2.54 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 198 HIS 0.003 0.001 HIS n 169 PHE 0.012 0.001 PHE m 180 TYR 0.019 0.001 TYR n 53 ARG 0.007 0.000 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 166) hydrogen bonds : angle 5.25644 ( 444) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.91329 ( 16) covalent geometry : bond 0.00228 ( 6780) covalent geometry : angle 0.53237 ( 9184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: m 46 GLU cc_start: 0.8183 (tt0) cc_final: 0.7767 (tt0) REVERT: m 137 ARG cc_start: 0.5766 (ptt-90) cc_final: 0.5405 (ptt90) REVERT: m 149 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6426 (mpp) REVERT: n 53 TYR cc_start: 0.8712 (t80) cc_final: 0.8336 (t80) REVERT: n 111 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5432 (t80) REVERT: M 125 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (mp) REVERT: M 131 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7030 (ttm-80) REVERT: M 161 GLU cc_start: 0.6408 (mt-10) cc_final: 0.5763 (mt-10) REVERT: M 170 ASN cc_start: 0.7701 (p0) cc_final: 0.7462 (p0) REVERT: M 191 LYS cc_start: 0.7098 (mppt) cc_final: 0.6273 (mppt) REVERT: N 43 GLU cc_start: 0.7731 (pp20) cc_final: 0.7422 (pp20) outliers start: 40 outliers final: 32 residues processed: 137 average time/residue: 0.2767 time to fit residues: 49.5872 Evaluate side-chains 136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 149 MET Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 77 ARG Chi-restraints excluded: chain n residue 91 ASN Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 218 HIS n 91 ASN n 218 ASN M 22 GLN M 102 GLN M 120 ASN N 210 HIS ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145096 restraints weight = 8743.838| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.69 r_work: 0.3492 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6788 Z= 0.202 Angle : 0.675 12.013 9200 Z= 0.348 Chirality : 0.050 0.211 1028 Planarity : 0.005 0.051 1144 Dihedral : 4.926 16.719 884 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 5.60 % Allowed : 20.13 % Favored : 74.27 % 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: -2.14 (0.28), residues: 808 helix: -3.22 (0.85), residues: 22 sheet: -0.26 (0.26), residues: 414 loop : -2.74 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 49 HIS 0.004 0.001 HIS n 210 PHE 0.019 0.002 PHE N 162 TYR 0.019 0.002 TYR n 53 ARG 0.006 0.001 ARG N 49 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 166) hydrogen bonds : angle 5.56634 ( 444) SS BOND : bond 0.00391 ( 8) SS BOND : angle 1.16235 ( 16) covalent geometry : bond 0.00483 ( 6780) covalent geometry : angle 0.67407 ( 9184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.850 Fit side-chains REVERT: m 46 GLU cc_start: 0.8196 (tt0) cc_final: 0.7697 (tt0) REVERT: M 131 ARG cc_start: 0.7250 (ttm110) cc_final: 0.6876 (ttm-80) REVERT: M 179 GLU cc_start: 0.7611 (tt0) cc_final: 0.7018 (mp0) REVERT: M 191 LYS cc_start: 0.7142 (mppt) cc_final: 0.6758 (mppt) outliers start: 42 outliers final: 37 residues processed: 136 average time/residue: 0.2255 time to fit residues: 41.0505 Evaluate side-chains 139 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 149 MET Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 193 ASN n 91 ASN M 22 GLN M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147401 restraints weight = 8757.751| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.69 r_work: 0.3519 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6788 Z= 0.131 Angle : 0.590 10.054 9200 Z= 0.305 Chirality : 0.047 0.217 1028 Planarity : 0.005 0.048 1144 Dihedral : 4.552 14.280 884 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.47 % Allowed : 20.00 % Favored : 74.53 % 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: -1.92 (0.28), residues: 808 helix: -2.96 (0.88), residues: 22 sheet: -0.13 (0.27), residues: 400 loop : -2.50 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 198 HIS 0.005 0.001 HIS n 169 PHE 0.011 0.002 PHE m 180 TYR 0.022 0.001 TYR n 53 ARG 0.007 0.000 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 166) hydrogen bonds : angle 5.42555 ( 444) SS BOND : bond 0.00240 ( 8) SS BOND : angle 1.07375 ( 16) covalent geometry : bond 0.00306 ( 6780) covalent geometry : angle 0.58873 ( 9184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.810 Fit side-chains REVERT: m 33 MET cc_start: 0.7387 (tpp) cc_final: 0.7135 (tpp) REVERT: m 46 GLU cc_start: 0.8207 (tt0) cc_final: 0.7708 (tt0) REVERT: m 149 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6131 (mpp) REVERT: n 111 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5342 (t80) REVERT: M 125 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8825 (mp) REVERT: M 131 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6922 (ttm-80) REVERT: M 161 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5940 (mt-10) REVERT: M 170 ASN cc_start: 0.7740 (p0) cc_final: 0.7327 (p0) REVERT: M 191 LYS cc_start: 0.7023 (mppt) cc_final: 0.6165 (mppt) outliers start: 41 outliers final: 33 residues processed: 138 average time/residue: 0.2857 time to fit residues: 54.4429 Evaluate side-chains 139 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 149 MET Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 218 HIS n 91 ASN M 22 GLN M 120 ASN M 193 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148009 restraints weight = 8751.473| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.40 r_work: 0.3523 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6788 Z= 0.138 Angle : 0.595 9.814 9200 Z= 0.308 Chirality : 0.048 0.232 1028 Planarity : 0.005 0.049 1144 Dihedral : 4.582 14.759 884 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 5.60 % Allowed : 19.87 % Favored : 74.53 % 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: -1.88 (0.28), residues: 808 helix: -2.72 (0.95), residues: 22 sheet: -0.15 (0.27), residues: 400 loop : -2.43 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 198 HIS 0.005 0.001 HIS n 169 PHE 0.013 0.002 PHE N 162 TYR 0.021 0.002 TYR n 53 ARG 0.007 0.001 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 166) hydrogen bonds : angle 5.41567 ( 444) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.05558 ( 16) covalent geometry : bond 0.00324 ( 6780) covalent geometry : angle 0.59384 ( 9184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.102 Fit side-chains REVERT: m 46 GLU cc_start: 0.8231 (tt0) cc_final: 0.7750 (tt0) REVERT: m 149 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6131 (mpp) REVERT: n 111 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.5375 (t80) REVERT: M 125 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8842 (mp) REVERT: M 131 ARG cc_start: 0.7263 (ttm110) cc_final: 0.6929 (ttm-80) REVERT: M 161 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6178 (mt-10) REVERT: M 170 ASN cc_start: 0.7783 (p0) cc_final: 0.7355 (p0) REVERT: M 179 GLU cc_start: 0.7524 (tt0) cc_final: 0.7021 (mp0) REVERT: M 191 LYS cc_start: 0.7075 (mppt) cc_final: 0.6715 (mppt) outliers start: 42 outliers final: 38 residues processed: 136 average time/residue: 0.2139 time to fit residues: 40.2053 Evaluate side-chains 144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 149 MET Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 77 ARG Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain n residue 111 TYR Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 91 ASN n 182 GLN M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143994 restraints weight = 8893.254| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.66 r_work: 0.3477 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6788 Z= 0.227 Angle : 0.703 12.609 9200 Z= 0.361 Chirality : 0.051 0.221 1028 Planarity : 0.005 0.057 1144 Dihedral : 5.070 16.484 884 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 5.87 % Allowed : 19.33 % Favored : 74.80 % 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: -2.01 (0.28), residues: 808 helix: -2.68 (0.97), residues: 22 sheet: -0.34 (0.27), residues: 404 loop : -2.40 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP n 198 HIS 0.005 0.001 HIS n 169 PHE 0.018 0.002 PHE N 162 TYR 0.024 0.002 TYR n 53 ARG 0.007 0.001 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 166) hydrogen bonds : angle 5.67740 ( 444) SS BOND : bond 0.00428 ( 8) SS BOND : angle 1.23797 ( 16) covalent geometry : bond 0.00548 ( 6780) covalent geometry : angle 0.70162 ( 9184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.639 Fit side-chains REVERT: m 46 GLU cc_start: 0.8220 (tt0) cc_final: 0.7733 (tt0) REVERT: M 125 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8833 (mp) REVERT: M 131 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6833 (ttm-80) REVERT: M 161 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6176 (mt-10) REVERT: M 179 GLU cc_start: 0.7602 (tt0) cc_final: 0.7021 (mp0) REVERT: M 191 LYS cc_start: 0.7203 (mppt) cc_final: 0.6749 (mppt) outliers start: 44 outliers final: 35 residues processed: 137 average time/residue: 0.1794 time to fit residues: 32.7272 Evaluate side-chains 136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 206 VAL Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 87 ASN Chi-restraints excluded: chain n residue 89 ILE Chi-restraints excluded: chain n residue 91 ASN Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 159 GLU Chi-restraints excluded: chain n residue 171 GLN Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 91 ASN n 182 GLN M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148020 restraints weight = 8772.954| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.38 r_work: 0.3521 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6788 Z= 0.139 Angle : 0.599 10.773 9200 Z= 0.312 Chirality : 0.048 0.230 1028 Planarity : 0.005 0.052 1144 Dihedral : 4.713 16.278 884 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.80 % Allowed : 20.80 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.28), residues: 808 helix: -2.42 (1.04), residues: 22 sheet: -0.21 (0.27), residues: 412 loop : -2.37 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP n 198 HIS 0.006 0.001 HIS n 169 PHE 0.012 0.002 PHE m 162 TYR 0.020 0.001 TYR n 53 ARG 0.007 0.001 ARG m 137 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 166) hydrogen bonds : angle 5.56124 ( 444) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.10049 ( 16) covalent geometry : bond 0.00324 ( 6780) covalent geometry : angle 0.59757 ( 9184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.82 seconds wall clock time: 82 minutes 37.80 seconds (4957.80 seconds total)