Starting phenix.real_space_refine on Tue Mar 3 17:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210.map" model { file = "/net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xjh_22210/03_2026/6xjh_22210_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5008 2.51 5 N 1210 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7596 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2030 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "C" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1736 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, D Time building chain proxies: 2.14, per 1000 atoms: 0.28 Number of scatterers: 7596 At special positions: 0 Unit cell: (75.98, 100.87, 106.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1334 8.00 N 1210 7.00 C 5008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 231.0 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 67.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid -4 through 15 Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 80 removed outlier: 3.562A pdb=" N VAL A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 132 through 162 Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.574A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Proline residue: A 179 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 191 through 200 removed outlier: 4.083A pdb=" N ASP A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 219 through 242 Processing helix chain 'B' and resid -3 through 15 Processing helix chain 'B' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 80 removed outlier: 3.563A pdb=" N VAL B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 89 through 126 Processing helix chain 'B' and resid 132 through 162 Processing helix chain 'B' and resid 164 through 186 removed outlier: 3.575A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 191 through 200 removed outlier: 4.084A pdb=" N ASP B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 219 through 242 Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 121 through 135 Processing helix chain 'C' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 21 removed outlier: 6.311A pdb=" N LYS C 8 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 6 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 19 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU C 4 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 21 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS C 2 " --> pdb=" O PHE C 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.437A pdb=" N LEU C 141 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER C 176 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 143 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 28 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL C 191 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY C 30 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 193 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 32 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 200 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG C 194 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 13 through 21 removed outlier: 6.310A pdb=" N LYS D 8 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 6 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 19 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU D 4 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE D 21 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS D 2 " --> pdb=" O PHE D 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.436A pdb=" N LEU D 141 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER D 176 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 143 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 28 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL D 191 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY D 30 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 193 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 32 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 200 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG D 194 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1536 1.32 - 1.47: 2716 1.47 - 1.61: 3434 1.61 - 1.75: 16 1.75 - 1.90: 52 Bond restraints: 7754 Sorted by residual: bond pdb=" C VAL D 199 " pdb=" N GLN D 200 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.45e-02 4.76e+03 1.59e+02 bond pdb=" C VAL C 199 " pdb=" N GLN C 200 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.45e-02 4.76e+03 1.58e+02 bond pdb=" CB HIS B 115 " pdb=" CG HIS B 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.10e+01 bond pdb=" CB GLN B 222 " pdb=" CG GLN B 222 " ideal model delta sigma weight residual 1.520 1.360 0.160 3.00e-02 1.11e+03 2.83e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 9533 2.66 - 5.32: 828 5.32 - 7.98: 105 7.98 - 10.65: 10 10.65 - 13.31: 6 Bond angle restraints: 10482 Sorted by residual: angle pdb=" N ILE B 167 " pdb=" CA ILE B 167 " pdb=" C ILE B 167 " ideal model delta sigma weight residual 111.58 104.54 7.04 1.06e+00 8.90e-01 4.41e+01 angle pdb=" N ILE A 167 " pdb=" CA ILE A 167 " pdb=" C ILE A 167 " ideal model delta sigma weight residual 111.58 104.55 7.03 1.06e+00 8.90e-01 4.40e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 120.37 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA PHE B 55 " pdb=" CB PHE B 55 " pdb=" CG PHE B 55 " ideal model delta sigma weight residual 113.80 120.34 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" C VAL B -4 " pdb=" N PRO B -3 " pdb=" CA PRO B -3 " ideal model delta sigma weight residual 119.56 126.19 -6.63 1.02e+00 9.61e-01 4.23e+01 ... (remaining 10477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 4490 22.45 - 44.89: 100 44.89 - 67.34: 18 67.34 - 89.78: 10 89.78 - 112.23: 2 Dihedral angle restraints: 4620 sinusoidal: 1880 harmonic: 2740 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.50 -112.23 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O1A AGS D 301 " pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " pdb=" PB AGS D 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.46 -112.19 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C ILE B 188 " pdb=" N ILE B 188 " pdb=" CA ILE B 188 " pdb=" CB ILE B 188 " ideal model delta harmonic sigma weight residual -122.00 -130.51 8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 673 0.067 - 0.134: 386 0.134 - 0.201: 124 0.201 - 0.268: 36 0.268 - 0.335: 11 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB VAL D 166 " pdb=" CA VAL D 166 " pdb=" CG1 VAL D 166 " pdb=" CG2 VAL D 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG D 189 " pdb=" N ARG D 189 " pdb=" C ARG D 189 " pdb=" CB ARG D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1227 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " -0.069 2.00e-02 2.50e+03 3.63e-02 2.63e+01 pdb=" CG TYR B 206 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.068 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR A 206 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 199 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL C 199 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 199 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN C 200 " -0.019 2.00e-02 2.50e+03 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 799 2.72 - 3.26: 8129 3.26 - 3.81: 12766 3.81 - 4.35: 16198 4.35 - 4.90: 26334 Nonbonded interactions: 64226 Sorted by model distance: nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 2.173 2.170 nonbonded pdb=" O2G AGS C 301 " pdb="MG MG C 302 " model vdw 2.173 2.170 nonbonded pdb=" N LYS D 39 " pdb=" O1B AGS D 301 " model vdw 2.257 3.120 nonbonded pdb=" N LYS C 39 " pdb=" O1B AGS C 301 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR D 40 " pdb="MG MG D 302 " model vdw 2.272 2.170 ... (remaining 64221 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.019 0.183 7754 Z= 1.071 Angle : 1.641 13.306 10482 Z= 1.126 Chirality : 0.095 0.335 1230 Planarity : 0.008 0.036 1264 Dihedral : 11.428 112.230 2852 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 0.95 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 928 helix: 1.29 (0.20), residues: 558 sheet: 1.10 (0.75), residues: 50 loop : -0.22 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 189 TYR 0.069 0.008 TYR B 206 PHE 0.030 0.006 PHE B 55 TRP 0.023 0.007 TRP A 223 HIS 0.007 0.002 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.01931 ( 7754) covalent geometry : angle 1.64065 (10482) hydrogen bonds : bond 0.15736 ( 483) hydrogen bonds : angle 6.87876 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 416 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TYR cc_start: 0.8034 (t80) cc_final: 0.7750 (t80) REVERT: A 115 HIS cc_start: 0.8383 (t-90) cc_final: 0.8132 (t-170) REVERT: A 122 VAL cc_start: 0.8548 (t) cc_final: 0.7827 (t) REVERT: A 130 ASN cc_start: 0.6500 (m-40) cc_final: 0.5963 (m-40) REVERT: A 166 MET cc_start: 0.7154 (mmp) cc_final: 0.5944 (ptp) REVERT: A 206 TYR cc_start: 0.7317 (p90) cc_final: 0.7026 (p90) REVERT: A 209 ASP cc_start: 0.7685 (t70) cc_final: 0.7293 (m-30) REVERT: A 220 ASN cc_start: 0.8146 (m-40) cc_final: 0.7892 (m110) REVERT: A 223 TRP cc_start: 0.7890 (t-100) cc_final: 0.7351 (t60) REVERT: A 243 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7855 (mmtt) REVERT: B 42 MET cc_start: 0.4106 (tpt) cc_final: 0.3120 (ptt) REVERT: B 70 VAL cc_start: 0.8394 (t) cc_final: 0.8049 (p) REVERT: B 106 LEU cc_start: 0.8455 (mm) cc_final: 0.8242 (mt) REVERT: B 115 HIS cc_start: 0.8191 (t-90) cc_final: 0.7622 (t-170) REVERT: B 122 VAL cc_start: 0.8676 (t) cc_final: 0.8405 (t) REVERT: B 209 ASP cc_start: 0.8031 (t70) cc_final: 0.7518 (m-30) REVERT: B 211 MET cc_start: 0.8414 (mtp) cc_final: 0.8115 (mtm) REVERT: B 220 ASN cc_start: 0.8352 (m-40) cc_final: 0.8095 (m110) REVERT: B 221 TRP cc_start: 0.8291 (m100) cc_final: 0.7873 (m100) REVERT: B 243 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8027 (mmtt) REVERT: C 3 LEU cc_start: 0.8564 (mt) cc_final: 0.8234 (mt) REVERT: C 43 MET cc_start: 0.8383 (mtm) cc_final: 0.8042 (mtp) REVERT: C 49 ASN cc_start: 0.8163 (m110) cc_final: 0.7927 (m-40) REVERT: C 56 LYS cc_start: 0.7501 (tttt) cc_final: 0.7300 (tptt) REVERT: C 58 ASP cc_start: 0.7504 (t0) cc_final: 0.7234 (t70) REVERT: C 63 ASP cc_start: 0.6664 (m-30) cc_final: 0.6408 (p0) REVERT: C 71 HIS cc_start: 0.7468 (m-70) cc_final: 0.6291 (m-70) REVERT: C 91 LEU cc_start: 0.8556 (mt) cc_final: 0.8300 (mp) REVERT: C 99 TYR cc_start: 0.8282 (t80) cc_final: 0.7900 (t80) REVERT: C 157 ASP cc_start: 0.8631 (m-30) cc_final: 0.8243 (t0) REVERT: C 172 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7140 (mmm160) REVERT: C 179 LYS cc_start: 0.8589 (mttt) cc_final: 0.8244 (mtpt) REVERT: D 56 LYS cc_start: 0.7046 (tttt) cc_final: 0.6676 (tppt) REVERT: D 58 ASP cc_start: 0.7537 (t0) cc_final: 0.7331 (m-30) REVERT: D 75 TYR cc_start: 0.7969 (m-80) cc_final: 0.7756 (m-10) REVERT: D 91 LEU cc_start: 0.8503 (mt) cc_final: 0.8190 (mp) REVERT: D 99 TYR cc_start: 0.8610 (t80) cc_final: 0.8217 (t80) REVERT: D 124 MET cc_start: 0.8329 (mtt) cc_final: 0.7844 (mtm) REVERT: D 157 ASP cc_start: 0.8154 (m-30) cc_final: 0.7851 (t0) REVERT: D 165 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt) REVERT: D 179 LYS cc_start: 0.8586 (mttt) cc_final: 0.8144 (mttp) REVERT: D 183 ILE cc_start: 0.8217 (mt) cc_final: 0.7937 (mt) REVERT: D 185 LEU cc_start: 0.8686 (tp) cc_final: 0.8458 (tt) REVERT: D 194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7549 (ttp80) outliers start: 4 outliers final: 0 residues processed: 416 average time/residue: 0.0830 time to fit residues: 46.3958 Evaluate side-chains 237 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 178 HIS C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 47 ASN D 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091750 restraints weight = 13795.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095266 restraints weight = 6950.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097685 restraints weight = 4467.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099077 restraints weight = 3328.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100209 restraints weight = 2772.963| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7754 Z= 0.208 Angle : 0.731 7.755 10482 Z= 0.396 Chirality : 0.049 0.197 1230 Planarity : 0.004 0.033 1264 Dihedral : 10.336 120.492 1040 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.75 % Allowed : 11.76 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 928 helix: 2.24 (0.21), residues: 556 sheet: 0.46 (0.67), residues: 58 loop : -0.38 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 189 TYR 0.026 0.002 TYR B 206 PHE 0.019 0.002 PHE C 23 TRP 0.024 0.002 TRP A 223 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7754) covalent geometry : angle 0.73087 (10482) hydrogen bonds : bond 0.06267 ( 483) hydrogen bonds : angle 5.10403 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.281 Fit side-chains REVERT: A 34 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7358 (mm-40) REVERT: A 51 TYR cc_start: 0.7193 (m-10) cc_final: 0.6684 (m-10) REVERT: A 141 TRP cc_start: 0.7848 (m100) cc_final: 0.7552 (m100) REVERT: A 166 MET cc_start: 0.6562 (mmp) cc_final: 0.5537 (ttm) REVERT: A 188 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5852 (mm) REVERT: A 220 ASN cc_start: 0.8186 (m-40) cc_final: 0.7957 (m110) REVERT: A 221 TRP cc_start: 0.8166 (m100) cc_final: 0.7945 (m100) REVERT: A 233 PHE cc_start: 0.8265 (m-80) cc_final: 0.7974 (m-80) REVERT: A 243 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7797 (mmtt) REVERT: B -2 ARG cc_start: 0.6406 (mtm-85) cc_final: 0.6071 (mmm160) REVERT: B 34 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6987 (mm-40) REVERT: B 87 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7348 (mmm) REVERT: B 115 HIS cc_start: 0.7805 (t-90) cc_final: 0.7559 (t-170) REVERT: B 122 VAL cc_start: 0.8671 (t) cc_final: 0.8163 (t) REVERT: B 139 ASN cc_start: 0.8066 (t0) cc_final: 0.7784 (t0) REVERT: B 152 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8653 (mm) REVERT: B 222 GLN cc_start: 0.7384 (tt0) cc_final: 0.7041 (mt0) REVERT: B 243 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7889 (mmtt) REVERT: C 4 GLU cc_start: 0.6925 (mp0) cc_final: 0.6523 (mp0) REVERT: C 43 MET cc_start: 0.8015 (mtm) cc_final: 0.7782 (mtt) REVERT: C 49 ASN cc_start: 0.8143 (m110) cc_final: 0.7907 (m-40) REVERT: C 58 ASP cc_start: 0.6805 (t0) cc_final: 0.6484 (t70) REVERT: C 70 GLU cc_start: 0.7608 (tp30) cc_final: 0.7291 (tp30) REVERT: C 71 HIS cc_start: 0.7059 (m-70) cc_final: 0.6686 (m90) REVERT: C 99 TYR cc_start: 0.8068 (t80) cc_final: 0.7580 (t80) REVERT: C 172 ARG cc_start: 0.7261 (mmt-90) cc_final: 0.6954 (mmm160) REVERT: C 181 GLU cc_start: 0.8329 (mp0) cc_final: 0.7949 (pm20) REVERT: D 64 ASN cc_start: 0.7610 (m-40) cc_final: 0.7321 (m110) REVERT: D 99 TYR cc_start: 0.8374 (t80) cc_final: 0.8137 (t80) REVERT: D 165 LEU cc_start: 0.8754 (mt) cc_final: 0.8541 (mt) REVERT: D 181 GLU cc_start: 0.8475 (mp0) cc_final: 0.7743 (pm20) REVERT: D 185 LEU cc_start: 0.8594 (tp) cc_final: 0.8310 (tt) REVERT: D 194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7552 (ttp80) outliers start: 40 outliers final: 29 residues processed: 308 average time/residue: 0.0722 time to fit residues: 31.3003 Evaluate side-chains 257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 220 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 285 ASN D 35 ASN D 71 HIS D 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092539 restraints weight = 13854.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095960 restraints weight = 6892.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098359 restraints weight = 4442.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099909 restraints weight = 3312.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101029 restraints weight = 2729.751| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7754 Z= 0.157 Angle : 0.640 7.776 10482 Z= 0.345 Chirality : 0.045 0.187 1230 Planarity : 0.004 0.034 1264 Dihedral : 10.062 112.492 1040 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.46 % Allowed : 16.03 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.27), residues: 928 helix: 2.05 (0.21), residues: 558 sheet: 0.14 (0.70), residues: 58 loop : -0.72 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.046 0.002 TYR A 206 PHE 0.028 0.002 PHE A 111 TRP 0.018 0.002 TRP A 223 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7754) covalent geometry : angle 0.64032 (10482) hydrogen bonds : bond 0.05287 ( 483) hydrogen bonds : angle 4.85970 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.7760 (m100) cc_final: 0.7386 (m100) REVERT: A 166 MET cc_start: 0.6218 (mmp) cc_final: 0.5290 (ttm) REVERT: A 204 PHE cc_start: 0.7348 (m-80) cc_final: 0.6163 (m-80) REVERT: A 220 ASN cc_start: 0.8087 (m-40) cc_final: 0.7812 (m110) REVERT: A 221 TRP cc_start: 0.7941 (m100) cc_final: 0.7696 (m100) REVERT: A 243 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7753 (mmtt) REVERT: B 51 TYR cc_start: 0.7109 (m-10) cc_final: 0.6768 (m-80) REVERT: B 84 GLN cc_start: 0.8441 (tt0) cc_final: 0.8120 (tt0) REVERT: B 87 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7168 (mmm) REVERT: B 115 HIS cc_start: 0.7781 (t-90) cc_final: 0.7532 (t-170) REVERT: B 152 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8635 (mm) REVERT: B 243 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7897 (mmtt) REVERT: C 2 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7276 (mtpp) REVERT: C 3 LEU cc_start: 0.8683 (mt) cc_final: 0.8124 (mp) REVERT: C 4 GLU cc_start: 0.6757 (mp0) cc_final: 0.6396 (mp0) REVERT: C 31 LEU cc_start: 0.8396 (tp) cc_final: 0.8017 (tt) REVERT: C 43 MET cc_start: 0.8001 (mtm) cc_final: 0.7423 (mtt) REVERT: C 49 ASN cc_start: 0.8203 (m110) cc_final: 0.7994 (m-40) REVERT: C 71 HIS cc_start: 0.7040 (m-70) cc_final: 0.6619 (m90) REVERT: C 99 TYR cc_start: 0.8102 (t80) cc_final: 0.7730 (t80) REVERT: C 144 ASP cc_start: 0.8042 (t0) cc_final: 0.7513 (t0) REVERT: C 181 GLU cc_start: 0.8418 (mp0) cc_final: 0.8042 (pm20) REVERT: C 200 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: D 56 LYS cc_start: 0.7260 (tmtt) cc_final: 0.7001 (tppt) REVERT: D 64 ASN cc_start: 0.7627 (m-40) cc_final: 0.7291 (m110) REVERT: D 102 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7683 (mttm) REVERT: D 124 MET cc_start: 0.8329 (mtm) cc_final: 0.8060 (mtm) REVERT: D 165 LEU cc_start: 0.8549 (mt) cc_final: 0.8317 (mt) REVERT: D 181 GLU cc_start: 0.8308 (mp0) cc_final: 0.7652 (pm20) REVERT: D 185 LEU cc_start: 0.8635 (tp) cc_final: 0.8308 (tt) REVERT: D 194 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7455 (ttp80) outliers start: 46 outliers final: 31 residues processed: 279 average time/residue: 0.0724 time to fit residues: 28.3340 Evaluate side-chains 261 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 139 ASN B 220 ASN C 89 GLN D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091945 restraints weight = 14059.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095286 restraints weight = 7056.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097618 restraints weight = 4546.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099160 restraints weight = 3397.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100156 restraints weight = 2795.401| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7754 Z= 0.145 Angle : 0.600 6.908 10482 Z= 0.323 Chirality : 0.044 0.180 1230 Planarity : 0.004 0.035 1264 Dihedral : 9.857 111.353 1040 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.34 % Allowed : 18.17 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 928 helix: 1.90 (0.21), residues: 560 sheet: 0.01 (0.70), residues: 58 loop : -1.04 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 194 TYR 0.039 0.002 TYR A 206 PHE 0.032 0.002 PHE B 143 TRP 0.014 0.001 TRP A 223 HIS 0.002 0.000 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7754) covalent geometry : angle 0.60031 (10482) hydrogen bonds : bond 0.04851 ( 483) hydrogen bonds : angle 4.77491 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8799 (tt0) cc_final: 0.8552 (mt0) REVERT: A 141 TRP cc_start: 0.7774 (m100) cc_final: 0.7385 (m100) REVERT: A 166 MET cc_start: 0.6050 (mmp) cc_final: 0.5390 (ttm) REVERT: A 204 PHE cc_start: 0.7368 (m-80) cc_final: 0.6140 (m-80) REVERT: A 220 ASN cc_start: 0.8146 (m-40) cc_final: 0.7920 (m110) REVERT: A 221 TRP cc_start: 0.7898 (m100) cc_final: 0.7608 (m100) REVERT: A 233 PHE cc_start: 0.8194 (m-80) cc_final: 0.7811 (m-80) REVERT: A 243 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7710 (mmtt) REVERT: B 51 TYR cc_start: 0.7091 (m-10) cc_final: 0.6825 (m-80) REVERT: B 84 GLN cc_start: 0.8426 (tt0) cc_final: 0.7989 (tp40) REVERT: B 87 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7254 (mmm) REVERT: B 152 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8647 (mm) REVERT: B 188 ILE cc_start: 0.6097 (mm) cc_final: 0.5752 (mt) REVERT: B 200 ASP cc_start: 0.8209 (m-30) cc_final: 0.7746 (t0) REVERT: B 243 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7901 (mmtt) REVERT: C 2 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7278 (mtpp) REVERT: C 4 GLU cc_start: 0.6783 (mp0) cc_final: 0.6343 (mp0) REVERT: C 71 HIS cc_start: 0.7003 (m-70) cc_final: 0.6636 (m90) REVERT: C 99 TYR cc_start: 0.8082 (t80) cc_final: 0.7695 (t80) REVERT: C 144 ASP cc_start: 0.8085 (t0) cc_final: 0.7552 (t0) REVERT: C 181 GLU cc_start: 0.8499 (mp0) cc_final: 0.8085 (pm20) REVERT: C 186 ILE cc_start: 0.8445 (mm) cc_final: 0.8234 (tt) REVERT: C 187 CYS cc_start: 0.6533 (t) cc_final: 0.5864 (p) REVERT: D 56 LYS cc_start: 0.7056 (tmtt) cc_final: 0.6740 (tppt) REVERT: D 124 MET cc_start: 0.8343 (mtm) cc_final: 0.7954 (mtm) REVERT: D 165 LEU cc_start: 0.8456 (mt) cc_final: 0.8206 (mt) REVERT: D 181 GLU cc_start: 0.8224 (mp0) cc_final: 0.7676 (pm20) REVERT: D 194 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7411 (ttp80) REVERT: D 285 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.6969 (t0) outliers start: 45 outliers final: 36 residues processed: 255 average time/residue: 0.0684 time to fit residues: 24.7169 Evaluate side-chains 256 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN C 89 GLN C 200 GLN D 35 ASN D 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092681 restraints weight = 14018.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096070 restraints weight = 7077.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098379 restraints weight = 4553.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099805 restraints weight = 3396.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100974 restraints weight = 2812.095| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7754 Z= 0.135 Angle : 0.597 6.843 10482 Z= 0.316 Chirality : 0.044 0.377 1230 Planarity : 0.004 0.034 1264 Dihedral : 9.617 108.762 1040 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.46 % Allowed : 19.12 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 928 helix: 1.74 (0.21), residues: 570 sheet: 0.08 (0.70), residues: 58 loop : -1.07 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.043 0.002 TYR A 206 PHE 0.019 0.001 PHE B 143 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7754) covalent geometry : angle 0.59702 (10482) hydrogen bonds : bond 0.04627 ( 483) hydrogen bonds : angle 4.72221 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.243 Fit side-chains REVERT: A 123 GLN cc_start: 0.8840 (tt0) cc_final: 0.8605 (mt0) REVERT: A 141 TRP cc_start: 0.7781 (m100) cc_final: 0.7397 (m100) REVERT: A 166 MET cc_start: 0.5901 (mmp) cc_final: 0.5180 (ttm) REVERT: A 204 PHE cc_start: 0.7271 (m-80) cc_final: 0.6166 (m-80) REVERT: A 220 ASN cc_start: 0.8222 (m-40) cc_final: 0.8020 (m110) REVERT: A 221 TRP cc_start: 0.7881 (m100) cc_final: 0.7640 (m100) REVERT: A 233 PHE cc_start: 0.8208 (m-80) cc_final: 0.7796 (m-80) REVERT: A 243 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7695 (mmtt) REVERT: B 15 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: B 51 TYR cc_start: 0.7029 (m-10) cc_final: 0.6829 (m-10) REVERT: B 84 GLN cc_start: 0.8407 (tt0) cc_final: 0.8003 (tp40) REVERT: B 87 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7252 (mmm) REVERT: B 152 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8631 (mm) REVERT: B 166 MET cc_start: 0.5396 (mmt) cc_final: 0.4662 (ttm) REVERT: B 188 ILE cc_start: 0.5943 (mm) cc_final: 0.5618 (mt) REVERT: B 200 ASP cc_start: 0.8150 (m-30) cc_final: 0.7809 (p0) REVERT: B 243 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7957 (mmtt) REVERT: B 245 ASP cc_start: 0.5081 (m-30) cc_final: 0.4835 (m-30) REVERT: C 2 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7378 (mtpp) REVERT: C 3 LEU cc_start: 0.8652 (mt) cc_final: 0.8447 (mt) REVERT: C 31 LEU cc_start: 0.8233 (tp) cc_final: 0.7947 (tt) REVERT: C 71 HIS cc_start: 0.6950 (m-70) cc_final: 0.6696 (m90) REVERT: C 99 TYR cc_start: 0.8130 (t80) cc_final: 0.7803 (t80) REVERT: C 181 GLU cc_start: 0.8518 (mp0) cc_final: 0.8090 (pm20) REVERT: C 186 ILE cc_start: 0.8468 (mm) cc_final: 0.8203 (tt) REVERT: C 187 CYS cc_start: 0.6313 (t) cc_final: 0.5723 (p) REVERT: C 194 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7435 (ttp80) REVERT: C 200 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6907 (mt0) REVERT: C 202 VAL cc_start: 0.7691 (t) cc_final: 0.7440 (m) REVERT: C 204 MET cc_start: 0.6223 (pmm) cc_final: 0.5903 (pmm) REVERT: D 124 MET cc_start: 0.8412 (mtm) cc_final: 0.7977 (mtm) REVERT: D 181 GLU cc_start: 0.8176 (mp0) cc_final: 0.7804 (pm20) REVERT: D 194 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7397 (ttp80) REVERT: D 278 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7868 (tpp80) REVERT: D 285 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.6808 (t0) outliers start: 46 outliers final: 28 residues processed: 249 average time/residue: 0.0719 time to fit residues: 25.4622 Evaluate side-chains 253 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092544 restraints weight = 14123.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095888 restraints weight = 7029.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098203 restraints weight = 4519.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099663 restraints weight = 3369.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100413 restraints weight = 2779.895| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7754 Z= 0.136 Angle : 0.584 8.033 10482 Z= 0.309 Chirality : 0.043 0.188 1230 Planarity : 0.004 0.034 1264 Dihedral : 9.417 106.210 1040 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.89 % Allowed : 17.81 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 928 helix: 1.77 (0.21), residues: 570 sheet: 0.06 (0.69), residues: 58 loop : -1.14 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.043 0.002 TYR A 206 PHE 0.017 0.001 PHE A 111 TRP 0.013 0.001 TRP A 223 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7754) covalent geometry : angle 0.58370 (10482) hydrogen bonds : bond 0.04481 ( 483) hydrogen bonds : angle 4.62726 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8817 (mp) REVERT: A 123 GLN cc_start: 0.8796 (tt0) cc_final: 0.8560 (mt0) REVERT: A 141 TRP cc_start: 0.7818 (m100) cc_final: 0.7409 (m100) REVERT: A 166 MET cc_start: 0.5831 (mmp) cc_final: 0.5160 (ttm) REVERT: A 174 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 204 PHE cc_start: 0.7408 (m-80) cc_final: 0.6294 (m-80) REVERT: A 220 ASN cc_start: 0.8132 (m-40) cc_final: 0.7910 (m110) REVERT: A 221 TRP cc_start: 0.7859 (m100) cc_final: 0.7618 (m100) REVERT: A 233 PHE cc_start: 0.8162 (m-80) cc_final: 0.7799 (m-80) REVERT: B 15 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: B 42 MET cc_start: 0.5620 (ptp) cc_final: 0.5044 (mtm) REVERT: B 84 GLN cc_start: 0.8418 (tt0) cc_final: 0.8024 (tp40) REVERT: B 87 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: B 116 TYR cc_start: 0.8204 (t80) cc_final: 0.7976 (t80) REVERT: B 152 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 166 MET cc_start: 0.5404 (mmt) cc_final: 0.4640 (ttm) REVERT: B 188 ILE cc_start: 0.5993 (mm) cc_final: 0.5633 (mt) REVERT: B 200 ASP cc_start: 0.8258 (m-30) cc_final: 0.7665 (t0) REVERT: B 243 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7977 (mmtt) REVERT: B 245 ASP cc_start: 0.5429 (m-30) cc_final: 0.5149 (m-30) REVERT: C 2 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7304 (mtpp) REVERT: C 3 LEU cc_start: 0.8583 (mt) cc_final: 0.8302 (mt) REVERT: C 4 GLU cc_start: 0.7171 (mp0) cc_final: 0.6689 (mp0) REVERT: C 70 GLU cc_start: 0.7705 (tp30) cc_final: 0.7237 (tp30) REVERT: C 71 HIS cc_start: 0.7071 (m-70) cc_final: 0.6606 (m90) REVERT: C 99 TYR cc_start: 0.8123 (t80) cc_final: 0.7744 (t80) REVERT: C 148 ASN cc_start: 0.7182 (t0) cc_final: 0.6936 (t0) REVERT: C 163 LYS cc_start: 0.8462 (tppt) cc_final: 0.8190 (ttmt) REVERT: C 181 GLU cc_start: 0.8475 (mp0) cc_final: 0.8162 (pm20) REVERT: C 194 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7362 (ttp80) REVERT: C 202 VAL cc_start: 0.7707 (t) cc_final: 0.7455 (m) REVERT: C 204 MET cc_start: 0.6449 (pmm) cc_final: 0.6143 (pmm) REVERT: D 4 GLU cc_start: 0.7698 (mp0) cc_final: 0.7238 (mp0) REVERT: D 124 MET cc_start: 0.8421 (mtm) cc_final: 0.7953 (mtm) REVERT: D 194 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7405 (ttp80) REVERT: D 278 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7913 (tpp80) REVERT: D 285 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.6611 (t0) outliers start: 58 outliers final: 42 residues processed: 251 average time/residue: 0.0655 time to fit residues: 23.5994 Evaluate side-chains 263 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091508 restraints weight = 14176.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094728 restraints weight = 7352.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096804 restraints weight = 4815.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098355 restraints weight = 3673.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098892 restraints weight = 3035.573| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7754 Z= 0.174 Angle : 0.609 6.724 10482 Z= 0.326 Chirality : 0.046 0.409 1230 Planarity : 0.004 0.036 1264 Dihedral : 9.388 101.426 1040 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 7.36 % Allowed : 17.81 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 928 helix: 1.71 (0.21), residues: 564 sheet: 0.05 (0.67), residues: 58 loop : -1.24 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 189 TYR 0.044 0.002 TYR A 206 PHE 0.018 0.001 PHE A 111 TRP 0.014 0.002 TRP A 223 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7754) covalent geometry : angle 0.60928 (10482) hydrogen bonds : bond 0.04541 ( 483) hydrogen bonds : angle 4.66084 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 31 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8860 (mp) REVERT: A 123 GLN cc_start: 0.8714 (tt0) cc_final: 0.8090 (mt0) REVERT: A 130 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7319 (m-40) REVERT: A 141 TRP cc_start: 0.7831 (m100) cc_final: 0.7441 (m100) REVERT: A 166 MET cc_start: 0.5884 (mmp) cc_final: 0.5322 (ttm) REVERT: A 220 ASN cc_start: 0.8060 (m-40) cc_final: 0.7832 (m110) REVERT: A 221 TRP cc_start: 0.7801 (m100) cc_final: 0.7554 (m100) REVERT: B 51 TYR cc_start: 0.6567 (m-10) cc_final: 0.6211 (m-80) REVERT: B 84 GLN cc_start: 0.8390 (tt0) cc_final: 0.8094 (tp40) REVERT: B 115 HIS cc_start: 0.7771 (t-170) cc_final: 0.7484 (t-170) REVERT: B 152 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8813 (mm) REVERT: B 166 MET cc_start: 0.5585 (mmt) cc_final: 0.4842 (ttm) REVERT: B 188 ILE cc_start: 0.6077 (mm) cc_final: 0.5747 (mt) REVERT: B 200 ASP cc_start: 0.8157 (m-30) cc_final: 0.7891 (p0) REVERT: C 1 MET cc_start: 0.6792 (tpp) cc_final: 0.6510 (tpt) REVERT: C 4 GLU cc_start: 0.7247 (mp0) cc_final: 0.6717 (mp0) REVERT: C 70 GLU cc_start: 0.7696 (tp30) cc_final: 0.7301 (tp30) REVERT: C 71 HIS cc_start: 0.7094 (m-70) cc_final: 0.6613 (m90) REVERT: C 99 TYR cc_start: 0.8106 (t80) cc_final: 0.7861 (t80) REVERT: C 181 GLU cc_start: 0.8432 (mp0) cc_final: 0.8161 (pm20) REVERT: D 4 GLU cc_start: 0.7697 (mp0) cc_final: 0.7265 (mp0) REVERT: D 124 MET cc_start: 0.8418 (mtm) cc_final: 0.7963 (mtm) REVERT: D 182 ASP cc_start: 0.7497 (m-30) cc_final: 0.7282 (p0) REVERT: D 194 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7480 (ttp80) REVERT: D 285 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.6489 (t0) outliers start: 62 outliers final: 45 residues processed: 257 average time/residue: 0.0665 time to fit residues: 24.5658 Evaluate side-chains 262 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 35 ASN D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.091204 restraints weight = 14271.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094355 restraints weight = 7110.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096636 restraints weight = 4611.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098072 restraints weight = 3440.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099100 restraints weight = 2844.691| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7754 Z= 0.132 Angle : 0.594 6.410 10482 Z= 0.317 Chirality : 0.044 0.194 1230 Planarity : 0.003 0.036 1264 Dihedral : 9.221 99.645 1040 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.82 % Allowed : 19.00 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 928 helix: 1.72 (0.21), residues: 570 sheet: -0.13 (0.70), residues: 50 loop : -1.27 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 287 TYR 0.045 0.001 TYR A 206 PHE 0.018 0.001 PHE A 111 TRP 0.033 0.002 TRP B 60 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7754) covalent geometry : angle 0.59450 (10482) hydrogen bonds : bond 0.04361 ( 483) hydrogen bonds : angle 4.63117 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.309 Fit side-chains REVERT: A 123 GLN cc_start: 0.8852 (tt0) cc_final: 0.8230 (mt0) REVERT: A 130 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: A 141 TRP cc_start: 0.7775 (m100) cc_final: 0.7431 (m100) REVERT: A 166 MET cc_start: 0.5756 (mmp) cc_final: 0.5125 (ttm) REVERT: A 220 ASN cc_start: 0.7971 (m-40) cc_final: 0.7759 (m110) REVERT: A 221 TRP cc_start: 0.7835 (m100) cc_final: 0.7595 (m100) REVERT: A 233 PHE cc_start: 0.8028 (m-80) cc_final: 0.7701 (m-80) REVERT: B 15 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: B 42 MET cc_start: 0.5786 (ptp) cc_final: 0.5188 (mtp) REVERT: B 84 GLN cc_start: 0.8436 (tt0) cc_final: 0.8089 (tp40) REVERT: B 87 MET cc_start: 0.8248 (mmm) cc_final: 0.7876 (mmm) REVERT: B 115 HIS cc_start: 0.7698 (t-170) cc_final: 0.7466 (t-170) REVERT: B 152 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (mm) REVERT: B 166 MET cc_start: 0.5373 (mmt) cc_final: 0.4513 (ttm) REVERT: B 188 ILE cc_start: 0.5945 (mm) cc_final: 0.5649 (mt) REVERT: B 200 ASP cc_start: 0.8166 (m-30) cc_final: 0.7714 (p0) REVERT: C 1 MET cc_start: 0.6585 (tpp) cc_final: 0.6158 (tpt) REVERT: C 2 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7360 (mtpp) REVERT: C 3 LEU cc_start: 0.8555 (mt) cc_final: 0.8185 (mt) REVERT: C 4 GLU cc_start: 0.7149 (mp0) cc_final: 0.6597 (mp0) REVERT: C 70 GLU cc_start: 0.7691 (tp30) cc_final: 0.7387 (tp30) REVERT: C 71 HIS cc_start: 0.7084 (m-70) cc_final: 0.6758 (m170) REVERT: C 181 GLU cc_start: 0.8601 (mp0) cc_final: 0.8289 (pm20) REVERT: C 194 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7170 (ttp80) REVERT: C 200 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: C 204 MET cc_start: 0.6503 (pmm) cc_final: 0.6268 (pmm) REVERT: D 4 GLU cc_start: 0.7744 (mp0) cc_final: 0.7305 (mp0) REVERT: D 124 MET cc_start: 0.8404 (mtm) cc_final: 0.7916 (mtm) REVERT: D 182 ASP cc_start: 0.7655 (m-30) cc_final: 0.7292 (p0) REVERT: D 194 ARG cc_start: 0.8086 (ttp-170) cc_final: 0.7492 (ttp80) REVERT: D 285 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6385 (t0) outliers start: 49 outliers final: 39 residues processed: 246 average time/residue: 0.0630 time to fit residues: 22.4793 Evaluate side-chains 258 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090978 restraints weight = 14180.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094162 restraints weight = 7145.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096410 restraints weight = 4664.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097789 restraints weight = 3518.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098704 restraints weight = 2939.503| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7754 Z= 0.140 Angle : 0.632 8.652 10482 Z= 0.331 Chirality : 0.045 0.200 1230 Planarity : 0.003 0.036 1264 Dihedral : 9.140 99.215 1040 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.82 % Allowed : 19.60 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 928 helix: 1.71 (0.21), residues: 570 sheet: 0.24 (0.68), residues: 58 loop : -1.36 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 278 TYR 0.046 0.002 TYR A 206 PHE 0.017 0.001 PHE A 111 TRP 0.017 0.002 TRP B 60 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7754) covalent geometry : angle 0.63185 (10482) hydrogen bonds : bond 0.04330 ( 483) hydrogen bonds : angle 4.61899 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.257 Fit side-chains REVERT: A 31 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 123 GLN cc_start: 0.8852 (tt0) cc_final: 0.8334 (mt0) REVERT: A 130 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7499 (m-40) REVERT: A 141 TRP cc_start: 0.7771 (m100) cc_final: 0.7432 (m100) REVERT: A 166 MET cc_start: 0.5762 (mmp) cc_final: 0.5145 (ttm) REVERT: A 204 PHE cc_start: 0.7460 (m-80) cc_final: 0.6276 (m-80) REVERT: A 220 ASN cc_start: 0.7974 (m-40) cc_final: 0.7770 (m110) REVERT: A 221 TRP cc_start: 0.7832 (m100) cc_final: 0.7598 (m100) REVERT: A 233 PHE cc_start: 0.8024 (m-80) cc_final: 0.7722 (m-80) REVERT: B 15 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: B 84 GLN cc_start: 0.8435 (tt0) cc_final: 0.8076 (tp40) REVERT: B 87 MET cc_start: 0.8433 (mmm) cc_final: 0.8199 (mmm) REVERT: B 115 HIS cc_start: 0.7725 (t-170) cc_final: 0.7505 (t-170) REVERT: B 152 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8540 (mm) REVERT: B 166 MET cc_start: 0.5403 (mmt) cc_final: 0.4447 (ttm) REVERT: B 188 ILE cc_start: 0.6037 (mm) cc_final: 0.5728 (mt) REVERT: C 1 MET cc_start: 0.6558 (tpp) cc_final: 0.6224 (tpt) REVERT: C 3 LEU cc_start: 0.8509 (mt) cc_final: 0.8117 (mt) REVERT: C 4 GLU cc_start: 0.7147 (mp0) cc_final: 0.6571 (mp0) REVERT: C 70 GLU cc_start: 0.7685 (tp30) cc_final: 0.7415 (tp30) REVERT: C 71 HIS cc_start: 0.7117 (m-70) cc_final: 0.6781 (m170) REVERT: C 181 GLU cc_start: 0.8566 (mp0) cc_final: 0.8270 (pm20) REVERT: C 285 ASN cc_start: 0.7690 (t0) cc_final: 0.7138 (t0) REVERT: D 103 ILE cc_start: 0.9039 (tp) cc_final: 0.8789 (tt) REVERT: D 124 MET cc_start: 0.8408 (mtm) cc_final: 0.7914 (mtm) REVERT: D 194 ARG cc_start: 0.8068 (ttp-170) cc_final: 0.7508 (ttp80) REVERT: D 285 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.6420 (t0) outliers start: 49 outliers final: 39 residues processed: 247 average time/residue: 0.0616 time to fit residues: 22.3445 Evaluate side-chains 260 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091478 restraints weight = 14166.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094565 restraints weight = 7109.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096866 restraints weight = 4665.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098148 restraints weight = 3502.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099309 restraints weight = 2932.561| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7754 Z= 0.139 Angle : 0.636 9.162 10482 Z= 0.333 Chirality : 0.044 0.194 1230 Planarity : 0.003 0.036 1264 Dihedral : 8.994 98.868 1040 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.34 % Allowed : 20.31 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 928 helix: 1.71 (0.21), residues: 570 sheet: 0.21 (0.69), residues: 58 loop : -1.38 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.046 0.002 TYR A 206 PHE 0.030 0.001 PHE B 218 TRP 0.009 0.001 TRP B 60 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7754) covalent geometry : angle 0.63567 (10482) hydrogen bonds : bond 0.04279 ( 483) hydrogen bonds : angle 4.63408 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.334 Fit side-chains REVERT: A 31 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 123 GLN cc_start: 0.8850 (tt0) cc_final: 0.8323 (mt0) REVERT: A 130 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7519 (m-40) REVERT: A 141 TRP cc_start: 0.7742 (m100) cc_final: 0.7408 (m100) REVERT: A 166 MET cc_start: 0.6019 (mmp) cc_final: 0.5186 (ttm) REVERT: A 221 TRP cc_start: 0.7833 (m100) cc_final: 0.7612 (m100) REVERT: B 15 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7199 (m-10) REVERT: B 84 GLN cc_start: 0.8441 (tt0) cc_final: 0.8085 (tp40) REVERT: B 152 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 166 MET cc_start: 0.5397 (mmt) cc_final: 0.4425 (ttm) REVERT: B 188 ILE cc_start: 0.6049 (mm) cc_final: 0.5781 (mt) REVERT: B 244 LYS cc_start: 0.7432 (tptt) cc_final: 0.7073 (ttpp) REVERT: C 1 MET cc_start: 0.6602 (tpp) cc_final: 0.6231 (tpt) REVERT: C 3 LEU cc_start: 0.8503 (mt) cc_final: 0.8295 (mt) REVERT: C 4 GLU cc_start: 0.7155 (mp0) cc_final: 0.6662 (mp0) REVERT: C 70 GLU cc_start: 0.7696 (tp30) cc_final: 0.7393 (tp30) REVERT: C 71 HIS cc_start: 0.7065 (m-70) cc_final: 0.6732 (m170) REVERT: C 181 GLU cc_start: 0.8556 (mp0) cc_final: 0.8336 (pm20) REVERT: C 200 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7074 (mt0) REVERT: C 285 ASN cc_start: 0.7637 (t0) cc_final: 0.7005 (t0) REVERT: D 124 MET cc_start: 0.8413 (mtm) cc_final: 0.7926 (mtm) REVERT: D 194 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7556 (ttp80) outliers start: 45 outliers final: 38 residues processed: 248 average time/residue: 0.0659 time to fit residues: 23.7930 Evaluate side-chains 259 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091602 restraints weight = 14075.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094760 restraints weight = 7129.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097007 restraints weight = 4664.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098345 restraints weight = 3507.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099512 restraints weight = 2931.226| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7754 Z= 0.141 Angle : 0.649 9.667 10482 Z= 0.339 Chirality : 0.047 0.451 1230 Planarity : 0.003 0.036 1264 Dihedral : 8.952 95.743 1040 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.23 % Allowed : 21.02 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 928 helix: 1.68 (0.21), residues: 570 sheet: 0.12 (0.68), residues: 58 loop : -1.46 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 189 TYR 0.044 0.002 TYR A 206 PHE 0.029 0.001 PHE B 218 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7754) covalent geometry : angle 0.64938 (10482) hydrogen bonds : bond 0.04258 ( 483) hydrogen bonds : angle 4.59518 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.15 seconds wall clock time: 22 minutes 43.73 seconds (1363.73 seconds total)