Starting phenix.real_space_refine on Fri Aug 22 17:56:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbv_36147/08_2025/8jbv_36147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbv_36147/08_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_36147/08_2025/8jbv_36147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbv_36147/08_2025/8jbv_36147.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbv_36147/08_2025/8jbv_36147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbv_36147/08_2025/8jbv_36147.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.70, per 1000 atoms: 0.26 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: 0.49 Conformation dependent library (CDL) restraints added in 308.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.28 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: 0.94 Time building geometry restraints manager: 0.63 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: 0.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- 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 : 4.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG m 36 TYR 0.022 0.003 TYR N 52 PHE 0.023 0.003 PHE n 162 TRP 0.011 0.002 TRP N 38 HIS 0.004 0.001 HIS N 74 Details of bonding type rmsd covalent geometry : bond 0.00816 ( 6780) covalent geometry : angle 1.12227 ( 9184) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.63900 ( 16) hydrogen bonds : bond 0.24296 ( 166) hydrogen bonds : angle 9.18024 ( 444) *********************** 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 : 0.152 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: 0.0881 time to fit residues: 26.9070 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 : 0.242 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 37 HIS n 91 ASN 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154620 restraints weight = 8545.660| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.11 r_work: 0.3616 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2715 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= 0.134 Angle : 0.636 11.007 9200 Z= 0.332 Chirality : 0.048 0.158 1028 Planarity : 0.005 0.040 1144 Dihedral : 8.340 58.048 916 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.67 % Allowed : 16.93 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.27), residues: 808 helix: -4.60 (0.43), residues: 22 sheet: -1.00 (0.26), residues: 418 loop : -2.99 (0.25), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 137 TYR 0.012 0.001 TYR M 200 PHE 0.013 0.002 PHE N 162 TRP 0.008 0.001 TRP n 79 HIS 0.002 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6780) covalent geometry : angle 0.63458 ( 9184) SS BOND : bond 0.00417 ( 8) SS BOND : angle 1.17653 ( 16) hydrogen bonds : bond 0.03907 ( 166) hydrogen bonds : angle 6.16286 ( 444) *********************** 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 149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: m 46 GLU cc_start: 0.8346 (tt0) cc_final: 0.8012 (tt0) REVERT: m 125 ILE cc_start: 0.8290 (mt) cc_final: 0.8070 (mt) REVERT: m 203 SER cc_start: 0.5967 (t) cc_final: 0.5759 (t) REVERT: n 111 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5165 (t80) REVERT: M 131 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6806 (ttm-80) REVERT: M 220 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7060 (m) outliers start: 35 outliers final: 26 residues processed: 141 average time/residue: 0.0737 time to fit residues: 13.9398 Evaluate side-chains 130 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 30 VAL 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 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 40 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 77 ASN N 210 HIS ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144738 restraints weight = 8638.327| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.31 r_work: 0.3481 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6788 Z= 0.244 Angle : 0.759 15.195 9200 Z= 0.390 Chirality : 0.052 0.195 1028 Planarity : 0.006 0.057 1144 Dihedral : 7.196 59.042 897 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 6.40 % Allowed : 18.27 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.27), residues: 808 helix: -4.47 (0.49), residues: 22 sheet: -0.72 (0.26), residues: 398 loop : -2.94 (0.25), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 49 TYR 0.018 0.002 TYR n 53 PHE 0.027 0.003 PHE N 162 TRP 0.014 0.002 TRP M 49 HIS 0.004 0.001 HIS n 37 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 6780) covalent geometry : angle 0.75736 ( 9184) SS BOND : bond 0.00686 ( 8) SS BOND : angle 1.37307 ( 16) hydrogen bonds : bond 0.04534 ( 166) hydrogen bonds : angle 6.15490 ( 444) *********************** 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 166 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: m 33 MET cc_start: 0.7457 (tpp) cc_final: 0.7188 (tpp) REVERT: m 46 GLU cc_start: 0.8175 (tt0) cc_final: 0.7780 (tt0) REVERT: n 111 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5751 (t80) REVERT: n 183 GLU cc_start: 0.8358 (mp0) cc_final: 0.8086 (mp0) REVERT: n 187 MET cc_start: 0.8203 (mtp) cc_final: 0.7958 (mtt) REVERT: M 131 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7010 (ttm-80) REVERT: M 206 VAL cc_start: 0.6498 (OUTLIER) cc_final: 0.6298 (p) REVERT: N 32 ASN cc_start: 0.8196 (p0) cc_final: 0.7889 (p0) REVERT: N 43 GLU cc_start: 0.7785 (pp20) cc_final: 0.7542 (pp20) REVERT: N 147 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7324 (ptmm) REVERT: N 148 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7551 (pp) outliers start: 48 outliers final: 34 residues processed: 151 average time/residue: 0.0831 time to fit residues: 16.5281 Evaluate side-chains 146 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 206 VAL Chi-restraints excluded: chain m residue 224 VAL 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 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 194 MET Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 206 VAL 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 48 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 148 LEU 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.172088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147185 restraints weight = 8700.583| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.27 r_work: 0.3531 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6788 Z= 0.135 Angle : 0.598 11.213 9200 Z= 0.311 Chirality : 0.047 0.187 1028 Planarity : 0.005 0.050 1144 Dihedral : 5.700 46.519 891 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.47 % Allowed : 18.93 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.28), residues: 808 helix: -4.11 (0.57), residues: 22 sheet: -0.40 (0.27), residues: 410 loop : -2.90 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 137 TYR 0.014 0.001 TYR n 53 PHE 0.011 0.002 PHE m 67 TRP 0.009 0.001 TRP M 49 HIS 0.004 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6780) covalent geometry : angle 0.59631 ( 9184) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.12404 ( 16) hydrogen bonds : bond 0.03384 ( 166) hydrogen bonds : angle 5.75072 ( 444) *********************** 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 147 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: m 33 MET cc_start: 0.7423 (tpp) cc_final: 0.7214 (tpp) REVERT: m 46 GLU cc_start: 0.8160 (tt0) cc_final: 0.7700 (tt0) REVERT: n 111 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5523 (t80) REVERT: M 131 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6888 (ttm-80) REVERT: M 161 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6148 (mt-10) REVERT: M 170 ASN cc_start: 0.7822 (p0) cc_final: 0.7429 (p0) REVERT: N 43 GLU cc_start: 0.7862 (pp20) cc_final: 0.7540 (pp20) REVERT: N 148 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7571 (pp) outliers start: 41 outliers final: 30 residues processed: 136 average time/residue: 0.0797 time to fit residues: 14.4816 Evaluate side-chains 131 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain m residue 146 VAL Chi-restraints excluded: chain m residue 178 THR Chi-restraints excluded: chain m residue 217 VAL Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain n residue 15 THR 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 188 LYS Chi-restraints excluded: chain n residue 200 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 148 LEU 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 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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 ** 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 = 0.3982 r_free = 0.3982 target = 0.171219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147266 restraints weight = 8738.070| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.33 r_work: 0.3507 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3796 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= 0.147 Angle : 0.605 10.882 9200 Z= 0.314 Chirality : 0.047 0.195 1028 Planarity : 0.005 0.050 1144 Dihedral : 5.384 38.643 889 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 6.80 % Allowed : 18.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.28), residues: 808 helix: -3.72 (0.70), residues: 22 sheet: -0.36 (0.27), residues: 414 loop : -2.85 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 137 TYR 0.016 0.002 TYR m 192 PHE 0.012 0.002 PHE N 196 TRP 0.011 0.001 TRP M 49 HIS 0.004 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6780) covalent geometry : angle 0.60367 ( 9184) SS BOND : bond 0.00292 ( 8) SS BOND : angle 1.07577 ( 16) hydrogen bonds : bond 0.03435 ( 166) hydrogen bonds : angle 5.60095 ( 444) *********************** 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 156 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 105 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: m 33 MET cc_start: 0.7408 (tpp) cc_final: 0.7166 (tpp) REVERT: m 46 GLU cc_start: 0.8166 (tt0) cc_final: 0.7714 (tt0) REVERT: n 111 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5333 (t80) REVERT: n 187 MET cc_start: 0.7980 (mtp) cc_final: 0.7691 (mtt) REVERT: M 76 GLN cc_start: 0.6835 (pm20) cc_final: 0.6456 (tt0) REVERT: M 131 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6912 (ttm-80) outliers start: 51 outliers final: 37 residues processed: 142 average time/residue: 0.0783 time to fit residues: 14.9026 Evaluate side-chains 140 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 217 VAL Chi-restraints excluded: chain m residue 224 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 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 98 CYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3988 r_free = 0.3988 target = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148215 restraints weight = 8745.091| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.27 r_work: 0.3529 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6788 Z= 0.140 Angle : 0.593 10.451 9200 Z= 0.309 Chirality : 0.047 0.207 1028 Planarity : 0.005 0.050 1144 Dihedral : 5.045 27.045 889 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.40 % Allowed : 18.67 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.28), residues: 808 helix: -3.42 (0.79), residues: 22 sheet: -0.31 (0.27), residues: 414 loop : -2.80 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 137 TYR 0.016 0.002 TYR n 53 PHE 0.011 0.002 PHE m 67 TRP 0.011 0.001 TRP n 198 HIS 0.004 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6780) covalent geometry : angle 0.59219 ( 9184) SS BOND : bond 0.00251 ( 8) SS BOND : angle 1.07039 ( 16) hydrogen bonds : bond 0.03352 ( 166) hydrogen bonds : angle 5.51531 ( 444) *********************** 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 154 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.267 Fit side-chains REVERT: m 33 MET cc_start: 0.7452 (tpp) cc_final: 0.7169 (tpt) REVERT: m 46 GLU cc_start: 0.8216 (tt0) cc_final: 0.7755 (tt0) REVERT: m 149 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6317 (mpp) REVERT: n 111 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5629 (t80) REVERT: n 187 MET cc_start: 0.8245 (mtp) cc_final: 0.7991 (mtt) REVERT: M 76 GLN cc_start: 0.6891 (pm20) cc_final: 0.6628 (tt0) REVERT: M 125 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8862 (mp) REVERT: M 131 ARG cc_start: 0.7404 (ttm110) cc_final: 0.6977 (ttm-80) REVERT: M 161 GLU cc_start: 0.6548 (mt-10) cc_final: 0.5977 (mt-10) REVERT: M 191 LYS cc_start: 0.7275 (mppt) cc_final: 0.6764 (mppt) outliers start: 48 outliers final: 42 residues processed: 141 average time/residue: 0.0888 time to fit residues: 16.5632 Evaluate side-chains 145 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 178 THR 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 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 91 ASN Chi-restraints excluded: chain n residue 98 CYS 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 188 LYS Chi-restraints excluded: chain n residue 194 MET 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 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 119 LEU 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 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 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 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.0010 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 overall best weight: 0.4344 ------------------------------------------------------------------------------- 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 ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4015 r_free = 0.4015 target = 0.174029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150375 restraints weight = 8734.163| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.31 r_work: 0.3552 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4051 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= 0.106 Angle : 0.548 8.854 9200 Z= 0.286 Chirality : 0.046 0.216 1028 Planarity : 0.005 0.046 1144 Dihedral : 4.503 25.442 886 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.87 % Allowed : 19.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.29), residues: 808 helix: -3.26 (0.83), residues: 22 sheet: -0.21 (0.27), residues: 416 loop : -2.69 (0.26), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 137 TYR 0.019 0.001 TYR n 193 PHE 0.011 0.001 PHE N 162 TRP 0.014 0.001 TRP n 198 HIS 0.004 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6780) covalent geometry : angle 0.54734 ( 9184) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.00276 ( 16) hydrogen bonds : bond 0.02996 ( 166) hydrogen bonds : angle 5.37541 ( 444) *********************** 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 151 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.256 Fit side-chains REVERT: m 46 GLU cc_start: 0.8200 (tt0) cc_final: 0.7715 (tt0) REVERT: m 149 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6354 (mpp) REVERT: n 111 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.5536 (t80) REVERT: n 187 MET cc_start: 0.8269 (mtp) cc_final: 0.8013 (mtt) REVERT: M 125 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8858 (mp) REVERT: M 131 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6937 (ttm-80) REVERT: M 161 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5859 (mt-10) REVERT: M 170 ASN cc_start: 0.7797 (p0) cc_final: 0.7385 (p0) REVERT: M 191 LYS cc_start: 0.7149 (mppt) cc_final: 0.6322 (mppt) outliers start: 44 outliers final: 35 residues processed: 139 average time/residue: 0.0786 time to fit residues: 14.5071 Evaluate side-chains 141 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 62 LEU 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 194 MET 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 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 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 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 72 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 218 ASN M 22 GLN M 102 GLN 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 = 0.3967 r_free = 0.3967 target = 0.169782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146395 restraints weight = 8781.047| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.23 r_work: 0.3507 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6788 Z= 0.178 Angle : 0.647 11.524 9200 Z= 0.334 Chirality : 0.049 0.213 1028 Planarity : 0.005 0.052 1144 Dihedral : 4.862 16.200 884 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 6.40 % Allowed : 19.60 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.28), residues: 808 helix: -3.10 (0.86), residues: 22 sheet: -0.28 (0.26), residues: 414 loop : -2.72 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 137 TYR 0.017 0.002 TYR N 52 PHE 0.015 0.002 PHE N 162 TRP 0.013 0.002 TRP n 198 HIS 0.004 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6780) covalent geometry : angle 0.64588 ( 9184) SS BOND : bond 0.00336 ( 8) SS BOND : angle 1.14197 ( 16) hydrogen bonds : bond 0.03646 ( 166) hydrogen bonds : angle 5.51871 ( 444) *********************** 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: 48 poor density : 101 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: m 33 MET cc_start: 0.7393 (tpp) cc_final: 0.7149 (tpp) REVERT: m 46 GLU cc_start: 0.8229 (tt0) cc_final: 0.7743 (tt0) REVERT: n 111 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5646 (t80) REVERT: M 125 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (mp) REVERT: M 131 ARG cc_start: 0.7384 (ttm110) cc_final: 0.6937 (ttm-80) outliers start: 48 outliers final: 43 residues processed: 136 average time/residue: 0.0757 time to fit residues: 14.0540 Evaluate side-chains 144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 178 THR 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 32 ASN 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 77 ARG 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 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 194 MET 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 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 187 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 216 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 32 ASN n 91 ASN ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3989 r_free = 0.3989 target = 0.171775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147413 restraints weight = 8780.400| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.27 r_work: 0.3537 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4140 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= 0.131 Angle : 0.586 9.976 9200 Z= 0.304 Chirality : 0.047 0.226 1028 Planarity : 0.005 0.049 1144 Dihedral : 4.630 14.987 884 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.27 % Allowed : 20.40 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.28), residues: 808 helix: -2.88 (0.91), residues: 22 sheet: -0.20 (0.27), residues: 414 loop : -2.66 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 137 TYR 0.019 0.002 TYR n 193 PHE 0.012 0.001 PHE m 180 TRP 0.015 0.001 TRP n 198 HIS 0.005 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6780) covalent geometry : angle 0.58463 ( 9184) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.07397 ( 16) hydrogen bonds : bond 0.03247 ( 166) hydrogen bonds : angle 5.43541 ( 444) *********************** 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 148 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.279 Fit side-chains REVERT: m 33 MET cc_start: 0.7422 (tpp) cc_final: 0.7165 (tpp) REVERT: m 46 GLU cc_start: 0.8198 (tt0) cc_final: 0.7700 (tt0) REVERT: n 111 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5559 (t80) REVERT: M 125 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8854 (mp) REVERT: M 131 ARG cc_start: 0.7324 (ttm110) cc_final: 0.6910 (ttm-80) REVERT: M 161 GLU cc_start: 0.6522 (mt-10) cc_final: 0.5892 (mt-10) REVERT: M 170 ASN cc_start: 0.7847 (p0) cc_final: 0.7418 (p0) REVERT: M 179 GLU cc_start: 0.7834 (tt0) cc_final: 0.7093 (mp0) REVERT: M 191 LYS cc_start: 0.7176 (mppt) cc_final: 0.6273 (mppt) outliers start: 47 outliers final: 42 residues processed: 136 average time/residue: 0.0794 time to fit residues: 14.5281 Evaluate side-chains 143 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 178 THR 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 32 ASN 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 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 194 MET Chi-restraints excluded: chain n residue 200 THR Chi-restraints excluded: chain M residue 25 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 119 LEU 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 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 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 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 68 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 32 ASN n 91 ASN ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.172390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148039 restraints weight = 8708.511| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.25 r_work: 0.3547 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4196 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= 0.120 Angle : 0.568 9.678 9200 Z= 0.296 Chirality : 0.047 0.230 1028 Planarity : 0.005 0.047 1144 Dihedral : 4.515 14.623 884 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.60 % Allowed : 20.80 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.29), residues: 808 helix: -2.70 (0.95), residues: 22 sheet: -0.11 (0.27), residues: 400 loop : -2.40 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 137 TYR 0.016 0.001 TYR n 193 PHE 0.012 0.001 PHE m 180 TRP 0.016 0.001 TRP n 198 HIS 0.005 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6780) covalent geometry : angle 0.56711 ( 9184) SS BOND : bond 0.00238 ( 8) SS BOND : angle 1.02905 ( 16) hydrogen bonds : bond 0.03158 ( 166) hydrogen bonds : angle 5.36954 ( 444) ********************** 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 144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 33 MET cc_start: 0.7429 (tpp) cc_final: 0.7173 (tpp) REVERT: m 46 GLU cc_start: 0.8214 (tt0) cc_final: 0.7712 (tt0) REVERT: n 111 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.5526 (t80) REVERT: n 187 MET cc_start: 0.8327 (mtt) cc_final: 0.8008 (mtp) REVERT: M 125 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8856 (mp) REVERT: M 131 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6949 (ttm-80) REVERT: M 161 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6124 (mt-10) REVERT: M 170 ASN cc_start: 0.7824 (p0) cc_final: 0.7402 (p0) REVERT: M 179 GLU cc_start: 0.7809 (tt0) cc_final: 0.7055 (mp0) outliers start: 42 outliers final: 37 residues processed: 134 average time/residue: 0.0755 time to fit residues: 13.4915 Evaluate side-chains 140 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 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 32 ASN 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 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 194 MET 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 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 15 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 32 ASN ** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 ASN ** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147439 restraints weight = 8710.741| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.16 r_work: 0.3545 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4226 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= 0.128 Angle : 0.576 10.081 9200 Z= 0.298 Chirality : 0.047 0.230 1028 Planarity : 0.005 0.048 1144 Dihedral : 4.531 15.321 884 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.87 % Allowed : 20.67 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.29), residues: 808 helix: -2.48 (1.00), residues: 22 sheet: -0.09 (0.27), residues: 400 loop : -2.39 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 215 TYR 0.019 0.001 TYR n 193 PHE 0.013 0.001 PHE m 180 TRP 0.016 0.001 TRP n 198 HIS 0.005 0.001 HIS n 169 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6780) covalent geometry : angle 0.57478 ( 9184) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.03246 ( 16) hydrogen bonds : bond 0.03188 ( 166) hydrogen bonds : angle 5.36782 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.69 seconds wall clock time: 34 minutes 34.84 seconds (2074.84 seconds total)